# HG changeset patch # User iuc # Date 1522854239 14400 # Node ID 81bbbddcf2854185680fdfcee1f09100afe0b05e # Parent 5e2a28bee02dcde43d257f392a77683ef00db1a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2 diff -r 5e2a28bee02d -r 81bbbddcf285 mageck_macros.xml --- a/mageck_macros.xml Sat Feb 17 10:41:53 2018 -0500 +++ b/mageck_macros.xml Wed Apr 04 11:03:59 2018 -0400 @@ -1,27 +1,34 @@ + 0.5.7 + mageck - + numpy r-gplots r-xtable + - mageck -v + /dev/null | grep -v -i "WARNING: ")", xtable version" $(R --vanilla --slave -e "library(xtable); cat(sessionInfo()\$otherPkgs\$xtable\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]> + + + + + + + + 10.1186/s13059-014-0554-4 - - - - - - diff -r 5e2a28bee02d -r 81bbbddcf285 mageck_test.xml --- a/mageck_test.xml Sat Feb 17 10:41:53 2018 -0500 +++ b/mageck_test.xml Wed Apr 04 11:03:59 2018 -0400 @@ -24,20 +24,39 @@ -n output $out.normcounts + $out.pdfreport ---norm-method $adv.norm_method ---gene-test-fdr-threshold $adv.fdr_threshold ---adjust-method $adv.adjust_method +#if $adv.norm_method: + --norm-method $adv.norm_method +#end if + +#if $adv.fdr_threshold: + --gene-test-fdr-threshold $adv.fdr_threshold +#end if + +#if $adv.adjust_method: + --adjust-method $adv.adjust_method +#end if + $adv.var_samples ---sort-criteria $adv.sort_criteria + +#if $adv.sort_criteria: + --sort-criteria $adv.sort_criteria +#end if ---remove-zero $adv.remove_zero +#if $adv.remove_zero: + --remove-zero $adv.remove_zero +#end if + #if $adv.remove_zero_threshold: --remove-zero-threshold $adv.remove_zero_threshold #end if ---gene-lfc-method $adv.lfc_method +#if $adv.lfc_method: + --gene-lfc-method $adv.lfc_method +#end if + #if $adv.control_sgrna: --control-sgrna $adv.control_sgrna #end if @@ -60,46 +79,50 @@ - + + ^[\w,]+$ + - + + ^[\w]+$ + - - + + ^[\w,]+$ +
- - + +
- + + - - - + + - + - - + + @@ -121,35 +144,41 @@ out['normcounts'] is True - + out['pdfreport'] is True - - out['rscriptOpt'] is True + + out['rfilesOpt'] is True + + + out['rfilesOpt'] is True - - - - + + + + + - - - - + + + + + - + - + + @@ -210,6 +239,18 @@ **Outputs** +This tool outputs + + * a ranked sgRNA Summary file + * a ranked Gene Summary file + +Optionally, under **Output Options** you can choose to output + + * a Normalized Counts table + * a PDF of the plots + * the .R and .Rnw files to generate the report + * a Log file of the analysis + **sgRNA Summary file** An example of the sgRNA ranking output is as follows: diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/in.test.sample.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.test.sample.txt Wed Apr 04 11:03:59 2018 -0400 @@ -0,0 +1,1000 @@ +sgRNA Gene HL60_initial KBM7_initial HL60_final KBM7_final +A1CF_m52595977 A1CF 213 274 883 175 +A1CF_m52596017 A1CF 294 412 1554 1891 +A1CF_m52596056 A1CF 421 368 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ACTN4 1160 610 1726 2233 +ACTN4_p39138476 ACTN4 306 268 1675 1709 +ACTN4_p39138482 ACTN4 927 566 2530 2890 +ACTR1A_m104248862 ACTR1A 719 1214 2213 2147 +ACTR1A_m104250350 ACTR1A 284 126 189 193 +ACTR1A_m104250365 ACTR1A 274 91 1128 1252 +ACTR1A_p104248833 ACTR1A 547 420 1032 1967 +ACTR1A_p104248866 ACTR1A 664 375 741 301 +ACTR1A_p104250290 ACTR1A 412 416 3242 1959 +ACTR1A_p104250304 ACTR1A 445 586 1731 2020 +ACTR1A_p104262351 ACTR1A 662 619 1218 4097 +ACTR1A_p104262374 ACTR1A 910 407 1189 1732 +ACTR1A_p104262383 ACTR1A 844 471 342 627 +ACTR3_m114684932 ACTR3 697 767 1401 693 +ACTR3_m114688941 ACTR3 781 589 1286 326 +ACTR3_p114674498 ACTR3 896 664 2125 1851 +ACTR3_p114684915 ACTR3 609 464 1110 998 +ACTR3_p114684941 ACTR3 648 616 1964 2548 +ACTR3_p114684946 ACTR3 524 309 1193 643 +ACTR3_p114684953 ACTR3 58 358 287 1091 +ACTR3_p114688931 ACTR3 491 433 927 1553 +ACTR3_p114691883 ACTR3 369 437 663 816 +ACTR3_p114691894 ACTR3 1477 1267 2229 2034 +ACTR5_m37377141 ACTR5 589 527 2529 2963 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432 381 1343 1621 +ACTRT3_m169487273 ACTRT3 549 406 282 1198 +ACTRT3_m169487289 ACTRT3 760 300 752 681 +ACTRT3_p169487206 ACTRT3 24 229 715 1043 +ACTRT3_p169487280 ACTRT3 1000 564 2005 1704 +ACVR1B_m52369170 ACVR1B 280 468 1538 2861 +ACVR1B_m52369187 ACVR1B 707 652 1605 1647 +ACVR1B_m52369192 ACVR1B 430 268 2364 748 +ACVR1B_m52369211 ACVR1B 1029 754 1684 2786 +ACVR1B_m52369226 ACVR1B 35 205 515 205 +ACVR1B_m52369237 ACVR1B 1002 865 1931 1920 +ACVR1B_p52369196 ACVR1B 276 160 275 415 +ACVR1B_p52369243 ACVR1B 471 422 963 783 +ACVR1B_p52369255 ACVR1B 114 94 70 263 +ACVR1B_p52369266 ACVR1B 796 679 2414 2199 +ACVR1C_m158401016 ACVR1C 305 258 723 1114 +ACVR1C_m158401030 ACVR1C 748 808 2126 3206 +ACVR1C_m158401075 ACVR1C 193 176 471 1063 +ACVR1C_m158401097 ACVR1C 654 444 1557 1665 +ACVR1C_m158401113 ACVR1C 224 185 486 717 +ACVR1C_m158443700 ACVR1C 675 359 1390 2446 +ACVR1C_m158443841 ACVR1C 323 290 1419 1520 +ACVR1C_p158443781 ACVR1C 335 259 1156 1715 +ACVR1C_p158443786 ACVR1C 959 517 2009 2015 +ACVR1C_p158443795 ACVR1C 1008 588 2106 2524 +ACVR1_m158637033 ACVR1 652 426 2567 2204 +ACVR1_m158637046 ACVR1 485 382 2055 1724 +ACVR1_m158637054 ACVR1 198 488 904 680 +ACVR1_m158637066 ACVR1 483 371 1070 1150 +ACVR1_m158655997 ACVR1 918 1304 2692 3010 +ACVR1_p158637019 ACVR1 455 605 1145 1331 +ACVR1_p158637035 ACVR1 1370 776 2676 3298 +ACVR1_p158637068 ACVR1 469 810 2288 2807 +ACVR1_p158655928 ACVR1 196 173 851 587 +ACVR1_p158655958 ACVR1 279 203 1070 569 +ACVR2A_m148602752 ACVR2A 955 561 1182 1126 +ACVR2A_m148602767 ACVR2A 1084 799 1782 3155 +ACVR2A_m148653941 ACVR2A 396 368 746 2145 +ACVR2A_m148653961 ACVR2A 587 243 1032 954 +ACVR2A_p148602720 ACVR2A 961 403 2354 3163 +ACVR2A_p148602754 ACVR2A 350 142 731 943 +ACVR2A_p148653859 ACVR2A 169 350 959 1370 +ACVR2A_p148653946 ACVR2A 648 263 1457 2080 +ACVR2A_p148653965 ACVR2A 390 95 190 583 +ACVR2A_p148653997 ACVR2A 1091 1020 2469 2845 +ACVR2B_m38495825 ACVR2B 1404 1332 3150 2677 +ACVR2B_m38518828 ACVR2B 275 617 2219 2134 +ACVR2B_m38518849 ACVR2B 440 415 1134 662 +ACVR2B_p38495805 ACVR2B 547 437 872 1040 +ACVR2B_p38495827 ACVR2B 789 618 1598 2756 +ACVR2B_p38518810 ACVR2B 780 728 2390 2354 +ACVR2B_p38518817 ACVR2B 861 991 2617 3970 +ACVR2B_p38518836 ACVR2B 997 438 1180 1663 +ACVR2B_p38518841 ACVR2B 400 279 1162 1254 +ACVR2B_p38518854 ACVR2B 1460 918 2715 3235 +ACVRL1_m52306276 ACVRL1 627 496 2249 2456 +ACVRL1_m52306307 ACVRL1 557 550 1651 1462 +ACVRL1_m52306881 ACVRL1 1133 621 2525 2059 +ACVRL1_m52306910 ACVRL1 868 640 2322 2264 +ACVRL1_m52306921 ACVRL1 504 296 2326 958 +ACVRL1_p52306245 ACVRL1 569 548 1736 2092 +ACVRL1_p52306281 ACVRL1 813 505 2675 2225 +ACVRL1_p52306287 ACVRL1 1148 859 2205 3686 +ACVRL1_p52306296 ACVRL1 906 633 1150 1272 +ACVRL1_p52306883 ACVRL1 1056 636 1842 2022 +ADAD1_m123301295 ADAD1 405 500 1518 1011 +ADAD1_m123301308 ADAD1 531 425 878 2224 +ADAD1_m123301332 ADAD1 711 630 1699 1668 +ADAD1_m123301345 ADAD1 350 264 1162 654 +ADAD1_m123301366 ADAD1 358 314 1423 1337 +ADAD1_p123301314 ADAD1 991 793 2078 2170 +ADAD1_p123301335 ADAD1 538 230 595 508 +ADAD1_p123301349 ADAD1 651 161 802 1162 +ADAD1_p123301358 ADAD1 1190 1074 3236 4172 +ADAD1_p123301373 ADAD1 628 471 1456 1346 +ADAM10_m58974490 ADAM10 417 394 676 702 +ADAM10_m59009777 ADAM10 367 575 1729 1785 +ADAM10_m59009866 ADAM10 415 353 538 1216 +ADAM10_m59009883 ADAM10 815 1060 2685 3758 +ADAM10_m59041689 ADAM10 61 56 79 309 +ADAM10_m59041696 ADAM10 340 258 649 592 +ADAM10_p58974401 ADAM10 659 487 936 448 +ADAM10_p58974481 ADAM10 911 649 2327 2141 +ADAM10_p59009761 ADAM10 246 134 293 508 +ADAM10_p59009767 ADAM10 603 423 1536 912 +ADAM12_m128018982 ADAM12 438 199 661 612 +ADAM12_m128019019 ADAM12 753 735 1714 1670 +ADAM12_m128019025 ADAM12 381 485 1516 1073 +ADAM12_m128076635 ADAM12 242 399 825 1111 +ADAM12_m128076658 ADAM12 523 432 2270 2731 +ADAM12_p128018991 ADAM12 35 39 132 389 +ADAM12_p128019039 ADAM12 1241 459 1049 1058 +ADAM12_p128076618 ADAM12 82 131 305 410 +ADAM12_p128076641 ADAM12 768 751 2339 3211 +ADAM12_p128076650 ADAM12 530 365 673 1328 +ADAMTS5_m28338537 ADAMTS5 668 722 1079 2252 +ADAMTS5_m28338697 ADAMTS5 727 422 859 1530 +ADAMTS5_m28338702 ADAMTS5 410 280 994 1053 +ADAMTS5_p28338524 ADAMTS5 614 586 1600 1039 +ADAMTS5_p28338585 ADAMTS5 662 529 853 1072 +ADAMTS5_p28338596 ADAMTS5 572 322 592 1002 +ADAMTS5_p28338607 ADAMTS5 758 530 2009 1206 +ADAMTS5_p28338612 ADAMTS5 78 166 278 479 +ADAMTS5_p28338620 ADAMTS5 272 118 566 822 +ADAMTS5_p28338667 ADAMTS5 759 520 1914 3378 +ADAP1_m975089 ADAP1 321 356 830 1158 +ADAP1_m975116 ADAP1 399 189 602 758 +ADAP1_m975132 ADAP1 651 530 1919 1445 +ADAP1_m994042 ADAP1 199 208 720 1240 +ADAP1_m994066 ADAP1 114 38 324 622 +ADAP1_m994071 ADAP1 781 405 416 603 +ADAP1_m994091 ADAP1 598 686 569 1671 +ADAP1_m994101 ADAP1 781 449 1441 1951 +ADAP1_m994106 ADAP1 300 372 1070 872 +ADAP1_p975103 ADAP1 619 400 837 2124 +ADARB1_m46591572 ADARB1 140 105 358 629 +ADARB1_m46595675 ADARB1 387 265 1117 697 +ADARB1_m46595697 ADARB1 485 319 952 1089 +ADARB1_m46595715 ADARB1 510 213 749 1177 +ADARB1_m46595721 ADARB1 156 414 1880 1598 +ADARB1_m46595779 ADARB1 453 98 304 253 +ADARB1_p46595645 ADARB1 738 566 2401 2617 +ADARB1_p46595700 ADARB1 503 515 1573 1321 +ADARB1_p46595705 ADARB1 1352 1069 2843 4330 +ADARB1_p46595724 ADARB1 234 73 485 397 +ADARB2_m1779246 ADARB2 1268 893 2792 2559 +ADARB2_m1779251 ADARB2 505 337 1496 1434 +ADARB2_m1779266 ADARB2 1067 1173 2870 3299 +ADARB2_m1779272 ADARB2 693 289 1077 1441 +ADARB2_m1779308 ADARB2 776 671 1395 1709 +ADARB2_m1779330 ADARB2 92 67 557 699 +ADARB2_m1779337 ADARB2 453 395 1564 1305 +ADARB2_p1421307 ADARB2 285 169 597 1128 +ADARB2_p1421336 ADARB2 382 306 1398 1015 +ADARB2_p1779233 ADARB2 301 129 627 1138 +ADAR_m154574098 ADAR 1070 579 1931 1523 +ADAR_m154574103 ADAR 90 75 441 1151 +ADAR_m154574108 ADAR 1085 615 2361 1748 +ADAR_m154574165 ADAR 458 292 865 1012 +ADAR_m154574219 ADAR 432 715 2566 1758 +ADAR_p154574043 ADAR 521 589 1702 1435 +ADAR_p154574114 ADAR 68 110 61 35 +ADAR_p154574121 ADAR 0 5 0 0 +ADAR_p154574126 ADAR 233 227 372 594 +ADAR_p154574157 ADAR 701 294 1072 1160 +ADCK1_m78285328 ADCK1 451 568 1746 2962 +ADCK1_m78285358 ADCK1 1053 1107 2964 4114 +ADCK1_m78285376 ADCK1 993 664 2055 2136 +ADCK1_m78285413 ADCK1 812 763 2571 3331 +ADCK1_p78285311 ADCK1 591 395 1142 1055 +ADCK1_p78285331 ADCK1 543 433 2344 3069 +ADCK1_p78285341 ADCK1 795 511 1394 1709 +ADCK1_p78285386 ADCK1 551 387 1076 1513 +ADCK1_p78285402 ADCK1 848 424 2063 2210 +ADCK1_p78285416 ADCK1 562 449 1550 3612 +ADCK2_m140373155 ADCK2 53 55 158 371 +ADCK2_m140373168 ADCK2 469 309 710 1295 +ADCK2_m140373177 ADCK2 396 453 1181 747 +ADCK2_m140373210 ADCK2 587 354 2377 1644 +ADCK2_m140373220 ADCK2 235 328 1346 846 +ADCK2_m140373231 ADCK2 894 647 1868 2104 +ADCK2_p140373122 ADCK2 394 525 1206 1142 +ADCK2_p140373137 ADCK2 132 30 193 44 +ADCK2_p140373158 ADCK2 570 537 1365 1700 +ADCK2_p140373194 ADCK2 854 572 2422 1834 +ADCK3_m227149096 ADCK3 184 234 688 919 +ADCK3_m227149144 ADCK3 179 95 300 405 +ADCK3_m227149153 ADCK3 844 1373 2964 3638 +ADCK3_m227149163 ADCK3 759 599 2130 3197 +ADCK3_p227149079 ADCK3 1573 613 2063 2888 +ADCK3_p227149104 ADCK3 1108 940 3375 3744 +ADCK3_p227149124 ADCK3 822 569 1637 1858 +ADCK3_p227149133 ADCK3 493 365 1114 1747 +ADCK3_p227149155 ADCK3 1548 1255 4648 5233 +ADCK3_p227149165 ADCK3 380 472 1686 2046 +ADCK4_m41220243 ADCK4 565 487 2139 1295 +ADCK4_m41220249 ADCK4 1008 1123 3240 3165 +ADCK4_m41220284 ADCK4 840 732 2152 3902 +ADCK4_m41220291 ADCK4 153 106 1110 142 +ADCK4_m41220465 ADCK4 553 476 1500 1747 +ADCK4_m41220474 ADCK4 1346 986 4215 4983 +ADCK4_m41220523 ADCK4 385 437 1392 779 +ADCK4_p41220276 ADCK4 463 301 873 1793 +ADCK4_p41220422 ADCK4 110 188 436 813 +ADCK4_p41220480 ADCK4 1717 1377 3413 2651 +ADCK5_m145603095 ADCK5 617 573 1345 2054 +ADCK5_m145603137 ADCK5 813 610 1046 1919 +ADCK5_m145603170 ADCK5 584 452 1694 958 +ADCK5_m145608301 ADCK5 715 396 2393 2309 +ADCK5_m145608343 ADCK5 637 445 2314 2374 +ADCK5_p145597774 ADCK5 392 305 1063 531 +ADCK5_p145603106 ADCK5 1009 755 3670 2825 +ADCK5_p145603142 ADCK5 871 833 2002 2685 +ADCK5_p145608305 ADCK5 256 349 597 165 +ADCK5_p145608311 ADCK5 409 418 1942 1575 +ADCY1_m45614206 ADCY1 122 176 649 351 +ADCY1_m45614243 ADCY1 688 682 769 1474 +ADCY1_m45614270 ADCY1 454 346 861 1526 +ADCY1_m45614323 ADCY1 483 514 1591 2080 +ADCY1_p45614127 ADCY1 1174 1279 2832 2521 +ADCY1_p45614255 ADCY1 307 465 1300 901 +ADCY1_p45614284 ADCY1 296 284 589 810 +ADCY1_p45614294 ADCY1 102 176 456 419 +ADCY1_p45614309 ADCY1 265 110 279 66 +ADCY1_p45614315 ADCY1 2 41 334 327 +ADD1_m2877698 ADD1 325 227 747 430 +ADD1_m2877722 ADD1 326 204 806 817 +ADD1_m2877771 ADD1 361 456 1293 1306 +ADD1_m2877776 ADD1 385 247 855 962 +ADD1_p2877627 ADD1 161 175 797 1406 +ADD1_p2877644 ADD1 558 574 1946 1334 +ADD1_p2877730 ADD1 132 14 378 366 +ADD1_p2877736 ADD1 751 456 1220 969 +ADD1_p2877743 ADD1 390 787 1155 1591 +ADD1_p2877761 ADD1 960 365 1696 1882 +ADD3_m111860427 ADD3 193 292 1082 1216 +ADD3_m111860445 ADD3 862 391 1646 934 +ADD3_m111860450 ADD3 1087 846 2617 3137 +ADD3_m111860456 ADD3 1010 495 2002 1201 +ADD3_m111860540 ADD3 794 741 2167 1575 +ADD3_p111860411 ADD3 404 470 829 1630 +ADD3_p111860500 ADD3 351 591 1798 1978 +ADD3_p111860505 ADD3 665 476 984 1023 +ADD3_p111860545 ADD3 940 681 1977 2029 +ADD3_p111860553 ADD3 1280 776 2512 1755 +ADH5_m100003154 ADH5 381 424 416 798 +ADH5_m100003254 ADH5 802 700 1376 1879 +ADH5_m100006267 ADH5 911 907 3313 3502 +ADH5_m100006354 ADH5 971 652 2604 2435 +ADH5_m100009841 ADH5 1322 1273 3324 3483 +ADH5_p100002504 ADH5 455 404 1225 1641 +ADH5_p100002510 ADH5 302 136 716 1270 +ADH5_p100002584 ADH5 1479 666 2178 2515 +ADH5_p100003219 ADH5 215 330 71 223 +ADH5_p100003224 ADH5 378 204 542 1124 +ADH7_m100349694 ADH7 552 581 1627 1566 +ADH7_m100350690 ADH7 116 403 581 668 +ADH7_m100350735 ADH7 553 374 1228 793 +ADH7_m100350762 ADH7 1263 889 2255 2111 +ADH7_p100349698 ADH7 740 477 1576 2712 +ADH7_p100349706 ADH7 316 222 272 956 +ADH7_p100349757 ADH7 412 324 814 1257 +ADH7_p100350692 ADH7 398 255 649 1596 +ADH7_p100350718 ADH7 117 181 363 114 +ADH7_p100350724 ADH7 233 217 712 560 +ADI1_m3517677 ADI1 282 275 359 706 +ADI1_m3523156 ADI1 523 407 1020 1658 +ADI1_m3523162 ADI1 403 400 575 1011 +ADI1_m3523239 ADI1 394 178 644 1113 +ADI1_m3523246 ADI1 545 375 1984 1698 +ADI1_m3523251 ADI1 1062 1025 3383 3536 +ADI1_p3517642 ADI1 178 225 644 1989 +ADI1_p3517660 ADI1 667 470 1496 1344 +ADI1_p3523164 ADI1 762 685 1012 1748 +ADI1_p3523171 ADI1 433 88 894 437 +ADIRF_m88728302 ADIRF 335 125 491 180 +ADIRF_m88728350 ADIRF 166 135 207 305 +ADIRF_m88729968 ADIRF 500 379 984 823 +ADIRF_p88728292 ADIRF 731 535 1745 1300 +ADIRF_p88728315 ADIRF 478 569 2047 1778 +ADIRF_p88728321 ADIRF 1121 428 1087 1063 +ADIRF_p88729942 ADIRF 647 487 962 1344 +ADIRF_p88729951 ADIRF 296 245 437 594 +ADIRF_p88729975 ADIRF 61 118 331 532 +ADIRF_p88729984 ADIRF 904 885 1780 2371 +ADK_m75960552 ADK 1002 1030 2002 2299 +ADK_m75960590 ADK 142 37 463 612 +ADK_m76153995 ADK 688 657 1035 1504 +ADK_m76154033 ADK 379 386 1387 1782 +ADK_p75960554 ADK 247 465 1168 611 +ADK_p76074446 ADK 1024 254 1036 1732 +ADK_p76074475 ADK 135 16 396 200 +ADK_p76074481 ADK 298 42 404 404 +ADK_p76153940 ADK 547 266 2118 2103 +ADK_p76154015 ADK 309 276 1421 1198 +ADNP2_m77891006 ADNP2 0 0 25 295 +ADNP2_p77875445 ADNP2 446 349 891 1167 +ADNP2_p77875475 ADNP2 169 60 454 806 +ADNP2_p77875482 ADNP2 382 220 761 1355 +ADNP2_p77875499 ADNP2 507 346 719 1609 +ADNP2_p77875511 ADNP2 880 734 1596 2475 +ADNP2_p77890985 ADNP2 528 721 1784 2201 +ADNP2_p77891013 ADNP2 505 342 833 1052 +ADNP2_p77891042 ADNP2 162 131 662 956 +ADNP2_p77891053 ADNP2 241 181 536 504 +ADNP_m49511043 ADNP 278 295 767 1226 +ADNP_m49518579 ADNP 1228 808 2714 3762 +ADNP_m49518587 ADNP 2053 1488 2908 6245 +ADNP_m49520451 ADNP 1122 441 1226 2328 +ADNP_m49520507 ADNP 653 787 2266 4913 +ADNP_p49510837 ADNP 337 170 534 970 +ADNP_p49510899 ADNP 1015 750 3309 3466 +ADNP_p49510949 ADNP 292 501 900 1980 +ADNP_p49511011 ADNP 291 323 1039 1572 +ADNP_p49520498 ADNP 470 432 1649 1736 +ADPRHL2_m36554512 ADPRHL2 337 456 1255 1717 +ADPRHL2_m36554557 ADPRHL2 1087 589 1204 1823 +ADPRHL2_m36554563 ADPRHL2 823 237 1247 1066 +ADPRHL2_m36554576 ADPRHL2 748 628 2075 2502 +ADPRHL2_m36554620 ADPRHL2 239 168 388 130 +ADPRHL2_p36554501 ADPRHL2 407 391 1071 1610 +ADPRHL2_p36554520 ADPRHL2 750 594 2176 1591 +ADPRHL2_p36554568 ADPRHL2 335 447 881 1510 +ADPRHL2_p36554580 ADPRHL2 578 527 1481 1293 +ADPRHL2_p36554606 ADPRHL2 175 138 84 355 +ADRA1A_m26722399 ADRA1A 110 130 597 857 +ADRA1A_m26722428 ADRA1A 0 0 108 322 +ADRA1A_m26722434 ADRA1A 716 734 1561 1900 +ADRA1A_m26722473 ADRA1A 552 327 1172 1094 +ADRA1A_p26722329 ADRA1A 1069 820 2273 2416 +ADRA1A_p26722406 ADRA1A 227 314 1002 1190 +ADRA1A_p26722412 ADRA1A 689 554 1599 1443 +ADRA1A_p26722419 ADRA1A 386 286 793 647 +ADRA1A_p26722438 ADRA1A 744 526 1152 1461 +ADRA1A_p26722465 ADRA1A 378 280 1518 394 +ADRA1B_m159343921 ADRA1B 46 138 311 193 +ADRA1B_m159343926 ADRA1B 358 462 1834 1238 +ADRA1B_m159343934 ADRA1B 509 676 1632 1313 +ADRA1B_m159343996 ADRA1B 509 295 1458 1358 +ADRA1B_m159344001 ADRA1B 224 174 1398 1182 +ADRA1B_m159344006 ADRA1B 341 125 345 760 +ADRA1B_m159344028 ADRA1B 731 297 1475 1304 +ADRA1B_p159343905 ADRA1B 279 165 70 585 +ADRA1B_p159343912 ADRA1B 782 825 1522 1899 +ADRA1B_p159343940 ADRA1B 731 705 2012 2117 +ADRB1_m115803922 ADRB1 157 126 616 620 +ADRB1_m115803930 ADRB1 300 124 716 632 +ADRB1_m115803938 ADRB1 588 662 1530 2374 +ADRB1_m115803996 ADRB1 439 290 1119 700 +ADRB1_m115804005 ADRB1 916 892 1255 1108 +ADRB1_m115804012 ADRB1 1474 1094 1733 1233 +ADRB1_m115804041 ADRB1 282 646 958 1752 +ADRB1_m115804047 ADRB1 434 307 611 563 +ADRB1_p115803878 ADRB1 298 647 2027 1533 +ADRB1_p115803909 ADRB1 393 357 1120 1694 +ADRB2_m148206406 ADRB2 564 485 1573 1390 +ADRB2_m148206447 ADRB2 562 463 1395 1143 +ADRB2_p148206408 ADRB2 731 425 2455 1785 +ADRB2_p148206418 ADRB2 302 232 732 632 +ADRB2_p148206432 ADRB2 318 630 939 939 +ADRB2_p148206450 ADRB2 414 494 1514 932 +ADRB2_p148206455 ADRB2 3368 2002 6329 7676 +ADRB2_p148206462 ADRB2 920 529 1751 2621 +ADRB2_p148206467 ADRB2 518 521 1030 1397 +ADRB2_p148206474 ADRB2 101 249 664 626 +ADRB3_m37823829 ADRB3 214 158 1095 887 +ADRB3_m37823842 ADRB3 97 0 0 242 +ADRB3_m37823867 ADRB3 171 134 398 767 +ADRB3_m37823894 ADRB3 827 1050 3426 3963 +ADRB3_p37823813 ADRB3 862 396 837 792 +ADRB3_p37823900 ADRB3 123 135 443 359 +ADRB3_p37823908 ADRB3 321 225 1162 1331 +ADRB3_p37823913 ADRB3 309 215 833 744 +ADRB3_p37823952 ADRB3 839 821 2409 2329 +ADRB3_p37823958 ADRB3 1511 550 2208 2013 +ADRBK1_m67034181 ADRBK1 253 494 3797 2735 +ADRBK1_m67034219 ADRBK1 755 641 1538 1746 +ADRBK1_m67034242 ADRBK1 995 681 2437 2655 +ADRBK1_m67034255 ADRBK1 399 556 1179 2293 +ADRBK1_p67034160 ADRBK1 693 404 1697 2000 +ADRBK1_p67034166 ADRBK1 864 683 2522 2840 +ADRBK1_p67034172 ADRBK1 899 1011 2344 2162 +ADRBK1_p67034193 ADRBK1 618 469 2599 2217 +ADRBK1_p67034199 ADRBK1 628 427 2345 2230 +ADRBK1_p67034261 ADRBK1 463 357 505 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AHCY 267 232 530 374 +AHCY_m32883330 AHCY 1367 1259 3863 3387 +AHCY_p32883227 AHCY 729 229 1023 611 +AHCY_p32883238 AHCY 42 123 974 791 +AHCY_p32883253 AHCY 443 495 376 33 +AHCY_p32883304 AHCY 1106 794 3402 3472 +AHCY_p32883309 AHCY 717 497 169 185 +AHNAK2_m105423801 AHNAK2 827 932 2364 2698 +AHNAK2_m105423809 AHNAK2 275 265 776 1124 +AHNAK2_m105423822 AHNAK2 215 414 1125 1162 +AHNAK2_m105423829 AHNAK2 502 495 890 704 +AHNAK2_m105423836 AHNAK2 200 460 2170 1886 +AHNAK2_m105444536 AHNAK2 260 256 1122 1064 +AHNAK2_m105444541 AHNAK2 518 374 1342 1589 +AHNAK2_m105444555 AHNAK2 343 156 257 1290 +AHNAK2_p105423957 AHNAK2 460 311 497 1143 +AHNAK2_p105423983 AHNAK2 247 219 1549 972 +AHNAK_m62303488 AHNAK 272 284 1238 1124 +AHNAK_m62303507 AHNAK 79 133 464 34 +AHNAK_m62303523 AHNAK 122 168 238 534 +AHNAK_m62303528 AHNAK 181 449 1074 1467 +AHNAK_m62303548 AHNAK 591 552 1143 573 +AHNAK_m62303560 AHNAK 479 540 1629 2630 +AHNAK_p62303470 AHNAK 258 412 1397 1743 +AHNAK_p62303477 AHNAK 446 282 879 831 +AHNAK_p62303510 AHNAK 322 254 948 862 +AHNAK_p62303551 AHNAK 35 23 186 55 +AHRR_m344006 AHRR 235 92 752 841 +AHRR_m344069 AHRR 283 210 337 610 +AHRR_m353878 AHRR 1 47 0 110 +AHRR_m353892 AHRR 239 85 458 728 +AHRR_m353898 AHRR 382 96 316 720 +AHRR_p344008 AHRR 171 125 2480 2626 +AHRR_p344030 AHRR 501 503 1767 803 +AHRR_p344036 AHRR 230 342 600 114 +AHRR_p344042 AHRR 837 296 1327 1652 diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count.R Wed Apr 04 11:03:59 2018 -0400 @@ -0,0 +1,5 @@ +Sweave("output_countsummary.Rnw"); +library(tools); + +texi2dvi("output_countsummary.tex",pdf=TRUE); + diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.Rnw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count.Rnw Wed Apr 04 11:03:59 2018 -0400 @@ -0,0 +1,237 @@ +% This is a template file for Sweave used in MAGeCK +% Author: Wei Li, Shirley Liu lab +% Do not modify lines beginning with "#__". +\documentclass{article} + +\usepackage{amsmath} +\usepackage{amscd} +\usepackage[tableposition=top]{caption} +\usepackage{ifthen} +\usepackage{fullpage} +\usepackage[utf8]{inputenc} +% \usepackage{longtable} + +\begin{document} +\setkeys{Gin}{width=0.9\textwidth} + +\title{MAGeCK Count Report} +\author{Wei Li} + +\maketitle + + +\tableofcontents + +\section{Summary} + +%Function definition +<>= +genreporttable<-function(filelist,labellist,reads,mappedreads){ + xtb=data.frame(Label=labellist,Reads=reads,MappedReads=mappedreads,MappedPercentage=mappedreads/reads); + colnames(xtb)=c("Label","Reads","Mapped","Percentage"); + return (xtb); +} +genreporttable2<-function(filelist,labellist,sgrnas,zerocounts,gini){ + xtb=data.frame(Label=labellist,TotalsgRNAs=sgrnas,ZeroCounts=zerocounts,GiniIndex=gini); + colnames(xtb)=c("Label","TotalsgRNA","ZeroCounts","GiniIndex"); + return (xtb); +} +genreporttable3<-function(filelist,labellist){ + xtb=data.frame(File=filelist,Label=labellist); + colnames(xtb)=c("File","Label"); + return (xtb); +} + + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F"); + + + +genboxplot<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + + boxplot(slmat_log,pch='.',las=2,ylab='log2(read counts)',cex.axis=0.8,...) +} + + +genhistplot<-function(filename,isfile=T,...){ + if(isfile){ + slmed=read.table(filename,header=T) + }else{ + slmed=filename; + } + tabsmat=as.matrix(log2(slmed[,c(-1,-2)]+1)) + colnames(tabsmat)=colnames(slmed)[c(-1,-2)] + samplecol=colors[((1:ncol(tabsmat)) %% length(colors)) ] + if(ncol(tabsmat)>=1){ + histlist=lapply(1:ncol(tabsmat),function(X){ return (hist(tabsmat[,X],plot=F,breaks=40)) }) + xrange=range(unlist(lapply(histlist,function(X){X$mids}))) + yrange=range(unlist(lapply(histlist,function(X){X$counts}))) + hst1=histlist[[1]] + plot(hst1$mids,hst1$counts,type='b',pch=20,xlim=c(0,xrange[2]*1.2),ylim=c(0,yrange[2]*1.2),xlab='log2(counts)',ylab='Frequency',main='Distribution of read counts',col = samplecol[1], ... ) + } + if(ncol(tabsmat)>=2){ + for(i in 2:ncol(tabsmat)){ + hstn=histlist[[i]] + lines(hstn$mids,hstn$counts,type='b',pch=20,col=samplecol[i]) + } + } + legend('topright',colnames(tabsmat),pch=20,lwd=1,col=samplecol) +} + + + +genclustering<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + + result=tryCatch({ + library(gplots); + heatmap.2(cor(slmat_log),trace = 'none',density.info = 'none',cexRow = 0.8,cexCol = 0.8,offsetRow = -0.2,offsetCol = -0.2) + }, error=function(e){ + heatmap(cor(slmat_log),scale='none',cexRow = 0.8,cexCol = 0.8,cex.axis=0.8,...) + }); +} + +ctfit_tx=0; + + +panel.plot<-function(x,y,textnames=names(x),...){ + par(new=TRUE) + m<-cbind(x,y) + plot(m,pch=20,xlim = range(x)*1.1,ylim=range(y)*1.1,...) + text(x,y,textnames,...) +} + + +genpcaplot<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + ctfit_tx<<-prcomp(t(slmat_log),center=TRUE) + + # par(mfrow=c(2,1)); + samplecol=colors[((1:ncol(slmat)) %% length(colors)) ] + # first 2 PCA + #plot(ctfit_tx$x[,1],ctfit_tx$x[,2],xlab='PC1',ylab='PC2',main='First 2 PCs',col=samplecol,xlim=1.1*range(ctfit_tx$x[,1]),ylim=1.1*range(ctfit_tx$x[,2])); + #text(ctfit_tx$x[,1],ctfit_tx$x[,2],rownames(ctfit_tx$x),col=samplecol); + # par(mfrow=c(1,1)); + if(length(samplecol)>2){ + pairs(ctfit_tx$x[,1:3],panel=panel.plot,textnames=rownames(ctfit_tx$x),main='First 3 principle components',col=samplecol) + }else{ + if(length(samplecol)>1){ + pairs(ctfit_tx$x[,1:2],panel=panel.plot,textnames=rownames(ctfit_tx$x),main='First 2 principle components',col=samplecol) + } + } + + +} + +genpcavar<-function(){ + # % variance + varpca=ctfit_tx$sdev^2 + varpca=varpca/sum(varpca)*100; + if(length(varpca)>10){ + varpca=varpca[1:10]; + } + plot(varpca,type='b',lwd=2,pch=20,xlab='PCs',ylab='% Variance explained'); +} + +@ + +%__FILE_SUMMARY__ + +The statistics of comparisons are listed in Table 1 and Table 2. +The corresponding fastq files in each row are listed in Table 3. + +<>= +library(xtable) +filelist=c("input_0.gz"); +labellist=c("test1_fastq_gz"); +reads=c(2500); +mappedreads=c(1453); +totalsgrnas=c(2550); +zerocounts=c(1276); +giniindex=c(0.5266899931488773); + +cptable=genreporttable(filelist,labellist,reads,mappedreads); +print(xtable(cptable, caption = "Summary of comparisons", label = "tab:one", + digits = c(0, 0, 0, 0,2), + align=c('c', 'c','c', 'c', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + +<>= +library(xtable) +cptable=genreporttable2(filelist,labellist,totalsgrnas,zerocounts,giniindex); +print(xtable(cptable, caption = "Summary of comparisons", label = "tab:two", + digits = c(0, 0,0, 0,2), + align=c('c', 'c','c', 'c', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + + + + + +<>= +library(xtable) +cptable=genreporttable3(filelist,labellist); +print(xtable(cptable, caption = "Summary of samples", label = "tab:three", + digits = c(0,0, 0), + align=c('c', 'p{9cm}', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + + + + +The meanings of the columns are as follows. + +\begin{itemize} +\item \textbf{Row}: The row number in the table; +\item \textbf{File}: The filename of fastq file; +\item \textbf{Label}: Assigned label; +\item \textbf{Reads}: The total read count in the fastq file; +\item \textbf{Mapped}: Reads that can be mapped to gRNA library; +\item \textbf{Percentage}: The percentage of mapped reads; +\item \textbf{TotalsgRNAs}: The number of sgRNAs in the library; +\item \textbf{ZeroCounts}: The number of sgRNA with 0 read counts; +\item \textbf{GiniIndex}: The Gini Index of the read count distribution. Gini index can be used to measure the evenness of the read counts, and a smaller value means a more even distribution of the read counts. +\end{itemize} + + + +\newpage\section{Normalized read count distribution of all samples} +The following figure shows the distribution of median-normalized read counts in all samples. + + +<>= +genboxplot("output.count_normalized.txt"); +@ + +The following figure shows the histogram of median-normalized read counts in all samples. + + +<>= +genhistplot("output.count_normalized.txt"); +@ + +%__INDIVIDUAL_PAGE__ + + + +\end{document} + diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.bam.txt --- a/test-data/out.count.bam.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.count.bam.txt Wed Apr 04 11:03:59 2018 -0400 @@ -1,4 +1,4 @@ -sgRNA Gene test1.bam +sgRNA Gene test1_bam s_10007 CCNA1 0 s_10008 CCNA1 0 s_10027 CCNC 0 diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.fastq.txt --- a/test-data/out.count.fastq.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.count.fastq.txt Wed Apr 04 11:03:59 2018 -0400 @@ -1,4 +1,4 @@ -sgRNA Gene test1.fastq.gz +sgRNA Gene test1_fastq_gz s_47512 RNF111 1 s_24835 HCFC1R1 1 s_14784 CYP4B1 4 diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.log.txt --- a/test-data/out.count.log.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.count.log.txt Wed Apr 04 11:03:59 2018 -0400 @@ -1,46 +1,43 @@ -INFO @ Wed, 14 Feb 2018 01:52:58: Parameters: /home/maria/miniconda3/envs/mulled-v1-0142cfe25b04f0c1d6899e250fb2f311b2d84778259938a0f6bd1d2ee743fa71/bin/mageck count -l /tmp/tmpqZ84Xc/files/000/dataset_7.dat --fastq input.gz -n output --pdf-report --keep-tmp --unmapped-to-file --norm-method median --sgrna-len 20 -INFO @ Wed, 14 Feb 2018 01:52:58: Welcome to MAGeCK v0.5.7. Command: count -INFO @ Wed, 14 Feb 2018 01:52:58: Loading 2550 predefined sgRNAs. -WARNING @ Wed, 14 Feb 2018 01:52:58: There are 0 sgRNAs with duplicated sequences. -INFO @ Wed, 14 Feb 2018 01:52:58: Parsing FASTQ file input.gz... -INFO @ Wed, 14 Feb 2018 01:52:58: Determining the trim-5 length of FASTQ file input.gz... -INFO @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20 -INFO @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads ... -INFO @ Wed, 14 Feb 2018 01:52:58: Read length:30 -INFO @ Wed, 14 Feb 2018 01:52:58: Total tested reads: 2500, mapped: 1453(0.5812) -INFO @ Wed, 14 Feb 2018 01:52:58: --trim-5 test data: (trim_length reads fraction) -INFO @ Wed, 14 Feb 2018 01:52:58: 0 1453 1.0 -INFO @ Wed, 14 Feb 2018 01:52:58: Auto determination of trim5 results: 0 -INFO @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20 -INFO @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads .. -INFO @ Wed, 14 Feb 2018 01:52:58: Total: 2500. -INFO @ Wed, 14 Feb 2018 01:52:58: Mapped: 1453. -DEBUG @ Wed, 14 Feb 2018 01:52:58: Initial (total) size factor: 1.0 -DEBUG @ Wed, 14 Feb 2018 01:52:58: Median factor: 2.0 -INFO @ Wed, 14 Feb 2018 01:52:58: Final size factor: 2.0 -INFO @ Wed, 14 Feb 2018 01:52:58: Summary of file input.gz: -INFO @ Wed, 14 Feb 2018 01:52:58: label sample1 -INFO @ Wed, 14 Feb 2018 01:52:58: reads 2500 -INFO @ Wed, 14 Feb 2018 01:52:58: mappedreads 1453 -INFO @ Wed, 14 Feb 2018 01:52:58: totalsgrnas 2550 -INFO @ Wed, 14 Feb 2018 01:52:58: zerosgrnas 1276 -INFO @ Wed, 14 Feb 2018 01:52:58: giniindex 0.5266899931488773 -INFO @ Wed, 14 Feb 2018 01:52:58: Loading Rnw template file: /home/maria/miniconda3/envs/mulled-v1-0142cfe25b04f0c1d6899e250fb2f311b2d84778259938a0f6bd1d2ee743fa71/lib/python3.6/site-packages/mageck/fastq_template.Rnw. -DEBUG @ Wed, 14 Feb 2018 01:52:58: Setting up the visualization module... -INFO @ Wed, 14 Feb 2018 01:52:58: Running command: cd ./; Rscript output_countsummary.R -INFO @ Wed, 14 Feb 2018 01:52:58: Command message: -INFO @ Wed, 14 Feb 2018 01:52:58: Writing to file output_countsummary.tex -INFO @ Wed, 14 Feb 2018 01:52:58: Processing code chunks with options ... -INFO @ Wed, 14 Feb 2018 01:52:58: 1 : keep.source term verbatim (label = funcdef, output_countsummary.Rnw:28) -INFO @ Wed, 14 Feb 2018 01:52:58: 2 : keep.source term tex (label = tab1, output_countsummary.Rnw:156) -INFO @ Wed, 14 Feb 2018 01:52:58: 3 : keep.source term tex (label = tab2, output_countsummary.Rnw:174) -INFO @ Wed, 14 Feb 2018 01:52:58: 4 : keep.source term tex (label = tab3, output_countsummary.Rnw:188) -INFO @ Wed, 14 Feb 2018 01:52:58: 5 : keep.source term verbatim pdf (output_countsummary.Rnw:221) -INFO @ Wed, 14 Feb 2018 01:52:58: 6 : keep.source term verbatim pdf (output_countsummary.Rnw:228) -INFO @ Wed, 14 Feb 2018 01:52:58: -INFO @ Wed, 14 Feb 2018 01:52:58: You can now run (pdf)latex on ‘output_countsummary.tex’ -INFO @ Wed, 14 Feb 2018 01:52:58: Error in texi2dvi("output_countsummary.tex", pdf = TRUE) : -INFO @ Wed, 14 Feb 2018 01:52:58: pdflatex is not available -INFO @ Wed, 14 Feb 2018 01:52:58: Execution halted -INFO @ Wed, 14 Feb 2018 01:52:58: -INFO @ Wed, 14 Feb 2018 01:52:58: End command message. +INFO @ Sun, 25 Mar 2018 15:51:06: Parameters: /Users/doylemaria/miniconda3/envs/mulled-v1-5ed9647f14e9d3e99564d31bed2eb19cd32ee8b9da66a89bea59b64a8983b1d6/bin/mageck count -l /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmp0EKzNL/files/000/dataset_2.dat --fastq input_0.gz --sample-label test1_fastq_gz -n output --pdf-report --keep-tmp --unmapped-to-file +INFO @ Sun, 25 Mar 2018 15:51:06: Welcome to MAGeCK v0.5.7. Command: count +INFO @ Sun, 25 Mar 2018 15:51:06: Loading 2550 predefined sgRNAs. +WARNING @ Sun, 25 Mar 2018 15:51:06: There are 0 sgRNAs with duplicated sequences. +INFO @ Sun, 25 Mar 2018 15:51:06: Parsing FASTQ file input_0.gz... +INFO @ Sun, 25 Mar 2018 15:51:06: Determining the trim-5 length of FASTQ file input_0.gz... +INFO @ Sun, 25 Mar 2018 15:51:06: Possible gRNA lengths:20 +INFO @ Sun, 25 Mar 2018 15:51:06: Processing 0M reads ... +INFO @ Sun, 25 Mar 2018 15:51:06: Read length:30 +INFO @ Sun, 25 Mar 2018 15:51:06: Total tested reads: 2500, mapped: 1453(0.5812) +INFO @ Sun, 25 Mar 2018 15:51:06: --trim-5 test data: (trim_length reads fraction) +INFO @ Sun, 25 Mar 2018 15:51:06: 0 1453 1.0 +INFO @ Sun, 25 Mar 2018 15:51:06: Auto determination of trim5 results: 0 +INFO @ Sun, 25 Mar 2018 15:51:06: Possible gRNA lengths:20 +INFO @ Sun, 25 Mar 2018 15:51:06: Processing 0M reads .. +INFO @ Sun, 25 Mar 2018 15:51:06: Total: 2500. +INFO @ Sun, 25 Mar 2018 15:51:06: Mapped: 1453. +DEBUG @ Sun, 25 Mar 2018 15:51:06: Initial (total) size factor: 1.0 +DEBUG @ Sun, 25 Mar 2018 15:51:06: Median factor: 2.0 +INFO @ Sun, 25 Mar 2018 15:51:06: Final size factor: 2.0 +INFO @ Sun, 25 Mar 2018 15:51:06: Summary of file input_0.gz: +INFO @ Sun, 25 Mar 2018 15:51:06: label test1_fastq_gz +INFO @ Sun, 25 Mar 2018 15:51:06: reads 2500 +INFO @ Sun, 25 Mar 2018 15:51:06: mappedreads 1453 +INFO @ Sun, 25 Mar 2018 15:51:06: totalsgrnas 2550 +INFO @ Sun, 25 Mar 2018 15:51:06: zerosgrnas 1276 +INFO @ Sun, 25 Mar 2018 15:51:06: giniindex 0.5266899931488773 +INFO @ Sun, 25 Mar 2018 15:51:06: Loading Rnw template file: /Users/doylemaria/miniconda3/envs/mulled-v1-5ed9647f14e9d3e99564d31bed2eb19cd32ee8b9da66a89bea59b64a8983b1d6/lib/python3.6/site-packages/mageck/fastq_template.Rnw. +DEBUG @ Sun, 25 Mar 2018 15:51:06: Setting up the visualization module... +INFO @ Sun, 25 Mar 2018 15:51:06: Running command: cd ./; Rscript output_countsummary.R +INFO @ Sun, 25 Mar 2018 15:51:11: Command message: +INFO @ Sun, 25 Mar 2018 15:51:11: Writing to file output_countsummary.tex +INFO @ Sun, 25 Mar 2018 15:51:11: Processing code chunks with options ... +INFO @ Sun, 25 Mar 2018 15:51:11: 1 : keep.source term verbatim (label = funcdef, output_countsummary.Rnw:28) +INFO @ Sun, 25 Mar 2018 15:51:11: 2 : keep.source term tex (label = tab1, output_countsummary.Rnw:156) +INFO @ Sun, 25 Mar 2018 15:51:11: 3 : keep.source term tex (label = tab2, output_countsummary.Rnw:174) +INFO @ Sun, 25 Mar 2018 15:51:11: 4 : keep.source term tex (label = tab3, output_countsummary.Rnw:188) +INFO @ Sun, 25 Mar 2018 15:51:11: 5 : keep.source term verbatim pdf (output_countsummary.Rnw:221) +INFO @ Sun, 25 Mar 2018 15:51:11: 6 : keep.source term verbatim pdf (output_countsummary.Rnw:228) +INFO @ Sun, 25 Mar 2018 15:51:11: +INFO @ Sun, 25 Mar 2018 15:51:11: You can now run (pdf)latex on ‘output_countsummary.tex’ +INFO @ Sun, 25 Mar 2018 15:51:11: +INFO @ Sun, 25 Mar 2018 15:51:11: End command message. diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count.txt Wed Apr 04 11:03:59 2018 -0400 @@ -0,0 +1,2551 @@ +sgRNA Gene test1_fastq_gz +s_47512 RNF111 1 +s_24835 HCFC1R1 1 +s_14784 CYP4B1 4 +s_51146 SLC18A1 1 +s_58960 TRIM5 1 +s_48256 RPRD2 1 +s_30297 KRTAP5-5 1 +s_14555 CYB5B 1 +s_39959 PAAF1 1 +s_45293 PUF60 1 +s_49358 SCN8A 1 +s_64995 ZYG11A 1 +s_4029 ASTE1 1 +s_45554 R3HDML 1 +s_34264 MMRN1 1 +s_37459 NOL6 1 +s_23990 GPX7 1 +s_20268 FANCC 1 +s_14157 CTLA4 1 +s_36773 NEURL4 18 +s_18804 ETFB 1 +s_782 ACSS1 1 +s_18272 ENPP2 1 +s_46620 RCN1 1 +s_55436 TAS2R3 1 +s_57947 TMPRSS2 1 +s_6438 C14orf159 1 +s_33846 MGST2 1 +s_16328 DNAH6 1 +s_17875 EIF4G1 1 +s_2305 ANAPC11 1 +s_2500 ANKRD2 1 +s_82 AARSD1 1 +s_55329 TAL1 1 +s_57926 TMPRSS11E 8 +s_38414 NUP98 4 +s_50044 SERPINF1 1 +s_9257 CASR 1 +s_63396 ZNF182 1 +s_56478 THBS3 1 +s_17191 DYRK1A 1 +s_11988 CIR1 1 +s_43313 PPARD 1 +s_44681 PSMA4 1 +s_10387 CD320 1 +s_64869 ZPBP 1 +s_54385 STK17B 1 +s_25423 HIST1H4D 1 +s_54172 ST8SIA4 9 +s_1161 ADCY10 1 +s_29184 KIAA0913 1 +s_42977 POLD3 1 +s_49449 SCUBE1 1 +s_24181 GRM4 1 +s_52507 SMARCA5 1 +s_28674 KCNJ10 1 +s_61074 VAMP2 4 +s_3954 ASIC2 1 +s_2385 ANK1 1 +s_18397 EPDR1 1 +s_18377 EPB41L4B 1 +s_34580 MRAP2 1 +s_48676 RUFY3 10 +s_691 ACP1 1 +s_30460 LAMP2 1 +s_42637 PLRG1 1 +s_12695 CNOT6 1 +s_33316 MECOM 2 +s_35081 MSRB2 1 +s_58512 TPD52L2 1 +s_19912 FAM22F 1 +s_45517 QSOX2 1 +s_56705 TINAG 1 +s_10946 CDKL5 1 +s_57473 TMEM211 2 +s_57657 TMEM44 1 +s_43200 POT1 1 +s_19436 FAM135A 1 +s_184 ABCB9 1 +s_30171 KRT84 1 +s_44758 PSMC3IP 1 +s_48313 RPS3 1 +s_58142 TNFSF12 6 +s_59718 TTLL6 7 +s_9725 CCDC43 1 +s_5135 BCKDHA 1 +s_36539 NDUFC2 1 +s_27251 IL27RA 1 +s_48939 SAMD10 1 +s_27343 IL5RA 1 +s_28386 KANK2 1 +s_27610 INSRR 1 +s_2769 AOC3 2 +s_58632 TRA2B 12 +s_6674 C16orf86 1 +s_22902 GJD4 1 +s_48278 RPS15A 1 +s_61998 WIPF2 1 +s_4937 BAIAP3 2 +s_54471 STOML1 2 +s_19157 FABP12 1 +s_5434 BIN1 2 +s_42042 PIP5K1A 1 +s_7794 C3orf18 1 +s_54846 SVIL 1 +s_62273 XPA 1 +s_45859 RACGAP1 1 +s_53626 SPOCK3 1 +s_43295 PPAP2C 7 +s_11788 CHRDL1 2 +s_50636 SHQ1 1 +s_16705 DPF1 1 +s_39741 OTOF 1 +s_27505 INHBE 1 +s_707 ACPL2 1 +s_15418 DDX3Y 6 +s_56018 TEAD4 1 +s_44367 PRR12 1 +s_25875 HOXB5 1 +s_49360 SCN9A 1 +s_16244 DMPK 1 +s_3909 ASCC2 1 +s_55088 SYT6 1 +s_54311 STAU1 1 +s_53890 SRP72 1 +s_11035 CDX1 1 +s_18178 EMR3 2 +s_16084 DLD 1 +s_47207 RHOBTB1 1 +s_40267 PARK2 6 +s_43104 POLR3B 1 +s_2200 AMDHD2 1 +s_12738 CNRIP1 1 +s_17842 EIF4A3 1 +s_57950 TMPRSS3 1 +s_62146 WRN 1 +s_11055 CEACAM1 1 +s_54580 STX2 1 +s_29277 KIAA1407 1 +s_33428 MEF2A 1 +s_59797 TUBB 1 +s_18113 EME1 1 +s_29839 KLHL8 1 +s_18058 ELP2 1 +s_49497 SDCBP2 3 +s_16874 DRP2 1 +s_13572 CREBL2 1 +s_20540 FBXO30 1 +s_64380 ZNF646 1 +s_50366 SH2B1 1 +s_2548 ANKRD33B 1 +s_41183 PDXP 1 +s_16315 DNAH12 1 +s_19996 FAM49B 1 +s_30751 LDLRAD3 1 +s_36960 NGEF 1 +s_39015 OR2A2 1 +s_26302 HSPB2 1 +s_64297 ZNF611 5 +s_730 ACSBG1 1 +s_50271 SFXN4 1 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1 +s_61437 VSIG1 1 +s_2427 ANKH 1 +s_48236 RPP25 1 +s_25248 HHIP 1 +s_49666 SEC61A2 2 +s_40916 PDE1C 1 +s_51267 SLC22A3 2 +s_45250 PTPRU 1 +s_54454 STMN2 1 +s_50448 SH3BP5 1 +s_35505 MYB 1 +s_34174 MMD2 1 +s_43046 POLR1D 1 +s_26919 IGSF1 1 +s_59350 TSKU 1 +s_52462 SMAD3 1 +s_44496 PRSS22 1 +s_12310 CLIC1 1 +s_60920 USP38 1 +s_42557 PLEKHO2 1 +s_37636 NPEPL1 1 +s_56222 TFAP2A 1 +s_46417 RBM22 1 +s_20477 FBXL6 1 +s_30504 LAPTM4A 1 +s_49873 4-Sep 1 +s_22231 GAPDH 1 +s_24866 HCRT 1 +s_26084 HRH4 1 +s_266 ABCG8 1 +s_31387 LPCAT1 1 +s_38114 NTF3 1 +s_13990 CST11 1 +s_24036 GRB14 1 +s_50585 SHISA4 1 +s_14163 CTNNA1 1 +s_1729 AK2 1 +s_62985 ZFHX3 1 +s_21318 FNBP1L 1 +s_13575 CREBRF 1 +s_5344 BET1 1 +s_49424 SCRN2 1 +s_31170 LIPN 1 +s_54781 SURF2 1 +s_51325 SLC25A1 1 +s_34136 MLNR 1 +s_31677 LRRC31 1 +s_53307 SPARCL1 1 +s_28022 ITGA7 1 +s_31356 LOXL3 1 +s_118 ABCA12 1 +s_12481 CLUL1 1 +s_40393 PAX3 1 +s_39614 OS9 1 +s_22342 GBA2 1 +s_1136 ADC 1 +s_10401 CD37 1 +s_4512 ATP7A 1 +s_10615 CDC27 1 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0 +s_41879 PIGR 0 +s_41955 PIK3CD 0 +s_42051 PIP5KL1 0 +s_42055 PIP5KL1 0 +s_42068 PISD 0 +s_42081 PITPNC1 0 +s_4209 ATL2 0 +s_42107 PITX3 0 +s_42123 PJA1 0 +s_42148 PKD2L2 0 +s_42162 PKHD1L1 0 +s_42181 PKM 0 +s_42215 PKP3 0 +s_4224 ATN1 0 +s_42243 PLA2G16 0 +s_42261 PLA2G2E 0 +s_42292 PLA2G5 0 +s_42305 PLA2R1 0 +s_42321 PLAC8L1 0 +s_42351 PLB1 0 +s_42366 PLCB2 0 +s_42392 PLCH1 0 +s_42446 PLEC 0 +s_42467 PLEKHA5 0 +s_42519 PLEKHG6 0 +s_42536 PLEKHM1 0 +s_42544 PLEKHM3 0 +s_42554 PLEKHO1 0 +s_42560 PLEKHS1 0 +s_42616 PLOD1 0 +s_42663 PLSCR5 0 +s_42751 PML 0 +s_42792 PNCK 0 +s_42839 PNN 0 +s_42932 PODXL2 0 +s_43016 POLK 0 +s_43060 POLR2C 0 +s_43122 POLR3G 0 +s_43155 POMT1 0 +s_43158 POMT1 0 +s_43253 POU6F2 0 +s_43302 PPAPDC1B 0 +s_43354 PPFIA1 0 +s_4339 ATP2C1 0 +s_43430 PPIL4 0 +s_43445 PPM1A 0 +s_43527 PPP1R12B 0 +s_43533 PPP1R13B 0 +s_43542 PPP1R14A 0 +s_43623 PPP1R3F 0 +s_43629 PPP1R42 0 +s_43789 PQLC2 0 +s_43834 PRAMEF13 0 +s_43837 PRAMEF16 0 +s_43862 PRB4 0 +s_4406 ATP5S 0 +s_44065 PRKACB 0 +s_44075 PRKAG2 0 +s_44091 PRKAR1B 0 +s_441 AC013461.1 0 +s_44162 PRKRA 0 +s_44181 PRLH 0 +s_44189 PRLR 0 +s_44260 PROKR1 0 +s_44270 PROM1 0 +s_44298 PRPF18 0 +s_44319 PRPF39 0 +s_44361 PRPSAP2 0 +s_44460 PRRT2 0 +s_44485 PRSS12 0 +s_4457 ATP6V0E2 0 +s_44634 PSG11 0 +s_44654 PSG8 0 +s_44726 PSMB5 0 +s_44739 PSMB8 0 +s_44746 PSMB9 0 +s_44782 PSMD13 0 +s_44808 PSMD8 0 +s_44910 PTCH1 0 +s_44935 PTCHD4 0 +s_45050 PTK2 0 +s_4507 ATP6V1H 0 +s_45113 PTPN12 0 +s_45128 PTPN18 0 +s_45139 PTPN22 0 +s_45141 PTPN22 0 +s_45165 PTPN7 0 +s_4523 ATP8A1 0 +s_45249 PTPRU 0 +s_45290 PUF60 0 +s_45296 PUM1 0 +s_45536 R3HCC1L 0 +s_45566 RAB11FIP1 0 +s_45586 RAB11FIP5 0 +s_45600 RAB15 0 +s_45601 RAB15 0 +s_45604 RAB17 0 +s_45627 RAB24 0 +s_45707 RAB3C 0 +s_45729 RAB3IP 0 +s_45763 RAB6A 0 +s_45796 RAB9B 0 +s_45894 RAD51AP1 0 +s_45908 RAD51C 0 +s_45960 RAI14 0 +s_45961 RAI14 0 +s_46068 RAP1GDS1 0 +s_46107 RAPH1 0 +s_46265 RASSF4 0 +s_46298 RAVER2 0 +s_46321 RBBP5 0 +s_46328 RBBP7 0 +s_46355 RBFOX3 0 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SLC2A6 0 +s_51660 SLC30A6 0 +s_51715 SLC35A4 0 +s_51729 SLC35B3 0 +s_51774 SLC35F3 0 +s_51783 SLC35G2 0 +s_51872 SLC39A14 0 +s_51904 SLC39A8 0 +s_52017 SLC4A2 0 +s_52093 SLC5A5 0 +s_52206 SLC7A14 0 +s_52255 SLC8A2 0 +s_52313 SLC9B1 0 +s_52364 SLCO4C1 0 +s_52383 SLFN13 0 +s_52421 SLITRK4 0 +s_52435 SLMO1 0 +s_52485 SMAP1 0 +s_5253 BCO2 0 +s_52574 SMCR8 0 +s_52587 SMG5 0 +s_52601 SMG7 0 +s_52617 SMO 0 +s_52642 SMPD4 0 +s_5268 BDH1 0 +s_52758 SNAPIN 0 +s_52784 SNIP1 0 +s_52787 SNIP1 0 +s_52833 SNRPB2 0 +s_52989 SNX8 0 +s_53 AAK1 0 +s_53048 SON 0 +s_53055 SORBS1 0 +s_53109 SOSTDC1 0 +s_53151 SOX30 0 +s_53153 SOX30 0 +s_53181 SP100 0 +s_53438 SPDYC 0 +s_53476 SPERT 0 +s_53512 SPI1 0 +s_53525 SPIN1 0 +s_53535 SPINK1 0 +s_53555 SPINK6 0 +s_53574 SPINT1 0 +s_53639 SPP1 0 +s_53691 SPRR3 0 +s_53740 SPTA1 0 +s_53830 SREK1 0 +s_53993 SSBP1 0 +s_54019 SSPN 0 +s_54054 SSTR5 0 +s_54078 ST14 0 +s_54092 ST3GAL3 0 +s_54099 ST3GAL3 0 +s_54292 STAT5A 0 +s_54305 STATH 0 +s_54314 STAU2 0 +s_54327 STC2 0 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TUBB2B 0 +s_59859 TULP1 0 +s_59870 TULP3 0 +s_59955 TXNDC8 0 +s_59983 TXNRD2 0 +s_600 ACE 0 +s_60169 UBE2H 0 +s_60209 UBE2Q2 0 +s_60237 UBE2V2 0 +s_60248 UBE3A 0 +s_60250 UBE3B 0 +s_60373 UBXN6 0 +s_60396 UCKL1 0 +s_60423 UEVLD 0 +s_60438 UFSP1 0 +s_60449 UGDH 0 +s_60517 UGT2A1 0 +s_60542 UGT3A1 0 +s_60603 UMODL1 0 +s_60614 UNC119 0 +s_60649 UNC5B 0 +s_6068 C10orf125 0 +s_6071 C10orf128 0 +s_60753 UQCRC2 0 +s_60780 URM1 0 +s_60839 USP15 0 +s_60851 USP19 0 +s_60925 USP4 0 +s_6100 C10orf53 0 +s_6106 C10orf54 0 +s_61149 VAV2 0 +s_61173 VCAM1 0 +s_61178 VCAN 0 +s_61221 VEPH1 0 +s_61263 VIL1 0 +s_61341 VPS13C 0 +s_61344 VPS13D 0 +s_61367 VPS29 0 +s_61529 VWA5A 0 +s_61531 VWA5A 0 +s_61587 WBP1 0 +s_61595 WBP2 0 +s_61623 WDFY1 0 +s_61640 WDHD1 0 +s_61662 WDR16 0 +s_61695 WDR26 0 +s_61739 WDR44 0 +s_6200 C11orf49 0 +s_62019 WISP1 0 +s_62098 WNT5B 0 +s_62114 WNT8A 0 +s_62171 WTAP 0 +s_62249 XKR3 0 +s_62257 XKR6 0 +s_62275 XPC 0 +s_62320 XRCC4 0 +s_62361 YAE1D1 0 +s_62550 ZBBX 0 +s_62559 ZBED6 0 +s_62567 ZBTB1 0 +s_62624 ZBTB37 0 +s_62657 ZBTB47 0 +s_62759 ZC3H7A 0 +s_62845 ZDHHC11 0 +s_62862 ZDHHC16 0 +s_62881 ZDHHC2 0 +s_6292 C12orf23 0 +s_62975 ZFC3H1 0 +s_63034 ZFP64 0 +s_63104 ZFYVE27 0 +s_63107 ZFYVE27 0 +s_63114 ZFYVE28 0 +s_63217 ZMIZ2 0 +s_63228 ZMYM3 0 +s_63234 ZMYM3 0 +s_6326 C12orf49 0 +s_63302 ZNF132 0 +s_63362 ZNF167 0 +s_63435 ZNF200 0 +s_63487 ZNF223 0 +s_63594 ZNF276 0 +s_636 ACO1 0 +s_63746 ZNF354B 0 +s_63755 ZNF362 0 +s_6376 C12orf74 0 +s_63903 ZNF436 0 +s_63905 ZNF438 0 +s_63923 ZNF442 0 +s_63934 ZNF445 0 +s_63935 ZNF446 0 +s_63964 ZNF469 0 +s_63983 ZNF480 0 +s_6409 C14orf105 0 +s_64137 ZNF554 0 +s_64241 ZNF586 0 +s_6427 C14orf133 0 +s_64356 ZNF639 0 +s_64393 ZNF655 0 +s_64396 ZNF655 0 +s_64419 ZNF668 0 +s_64424 ZNF669 0 +s_64459 ZNF682 0 +s_64479 ZNF688 0 +s_64581 ZNF746 0 +s_64627 ZNF772 0 +s_64638 ZNF776 0 +s_64652 ZNF780A 0 +s_64791 ZNF85 0 +s_64851 ZNRF3 0 +s_64871 ZPBP 0 +s_64878 ZPLD1 0 +s_64898 ZSCAN10 0 +s_64930 ZSCAN30 0 +s_64997 ZYG11A 0 +s_6525 C15orf39 0 +s_6592 C16orf13 0 +s_6639 C16orf62 0 +s_6707 C17orf102 0 +s_6710 C17orf104 0 +s_6728 C17orf112 0 +s_6736 C17orf39 0 +s_6794 C17orf72 0 +s_6814 C17orf80 0 +s_6849 C18orf21 0 +s_6859 C18orf32 0 +s_6862 C18orf34 0 +s_6906 C19orf38 0 +s_7053 C1QTNF7 0 +s_7128 C1orf122 0 +s_7144 C1orf130 0 +s_7162 C1orf144 0 +s_7234 C1orf198 0 +s_7341 C1orf63 0 +s_747 ACSL1 0 +s_76 AARS2 0 +s_7674 C2orf57 0 +s_7681 C2orf62 0 +s_7692 C2orf63 0 +s_77 AARSD1 0 +s_78 AARSD1 0 +s_781 ACSS1 0 +s_786 ACSS2 0 +s_7940 C4orf26 0 +s_7970 C4orf37 0 +s_8000 C4orf52 0 +s_804 ACTB 0 +s_8073 C5orf51 0 +s_8141 C6orf162 0 +s_8227 C7orf10 0 +s_8281 C7orf59 0 +s_8318 C8A 0 +s_8403 C9orf100 0 +s_8470 C9orf24 0 +s_8699 CACNA1G 0 +s_8705 CACNA1I 0 +s_871 ACTR8 0 +s_874 ACTR8 0 +s_8757 CACNG5 0 +s_8797 CADPS 0 +s_8879 CALR 0 +s_8910 CAMK2B 0 +s_893 ACVR1B 0 +s_8930 CAMKK1 0 +s_8954 CAMSAP1 0 +s_9064 CAPRIN1 0 +s_9077 CAPSL 0 +s_9109 CARD17 0 +s_913 ACY1 0 +s_9171 CASD1 0 +s_9196 CASP10 0 +s_9285 CATSPER3 0 +s_9506 CCDC120 0 +s_9507 CCDC121 0 +s_952 ADAM12 0 +s_9584 CCDC149 0 +s_964 ADAM18 0 +s_9646 CCDC170 0 +s_9710 CCDC40 0 +s_9732 CCDC48 0 +s_976 ADAM21 0 +s_9763 CCDC62 0 +s_9868 CCDC89 0 +s_991 ADAM30 0 +s_9925 CCL1 0 +s_9973 CCL26 0 diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.count_multi.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.count_multi.txt Wed Apr 04 11:03:59 2018 -0400 @@ -0,0 +1,2551 @@ +sgRNA Gene test1_fastq_gz test2_fastq_gz +s_47512 RNF111 1 0 +s_24835 HCFC1R1 1 0 +s_14784 CYP4B1 4 0 +s_51146 SLC18A1 1 0 +s_58960 TRIM5 1 0 +s_48256 RPRD2 1 0 +s_30297 KRTAP5-5 1 0 +s_14555 CYB5B 1 0 +s_39959 PAAF1 1 1 +s_45293 PUF60 1 0 +s_49358 SCN8A 1 1 +s_64995 ZYG11A 1 0 +s_4029 ASTE1 1 0 +s_45554 R3HDML 1 0 +s_34264 MMRN1 1 0 +s_37459 NOL6 1 0 +s_23990 GPX7 1 0 +s_20268 FANCC 1 0 +s_14157 CTLA4 1 0 +s_36773 NEURL4 18 3 +s_18804 ETFB 1 0 +s_782 ACSS1 1 0 +s_18272 ENPP2 1 0 +s_46620 RCN1 1 0 +s_55436 TAS2R3 1 0 +s_57947 TMPRSS2 1 1 +s_6438 C14orf159 1 0 +s_33846 MGST2 1 0 +s_16328 DNAH6 1 0 +s_17875 EIF4G1 1 0 +s_2305 ANAPC11 1 0 +s_2500 ANKRD2 1 0 +s_82 AARSD1 1 0 +s_55329 TAL1 1 0 +s_57926 TMPRSS11E 8 0 +s_38414 NUP98 4 0 +s_50044 SERPINF1 1 0 +s_9257 CASR 1 0 +s_63396 ZNF182 1 0 +s_56478 THBS3 1 0 +s_17191 DYRK1A 1 0 +s_11988 CIR1 1 0 +s_43313 PPARD 1 0 +s_44681 PSMA4 1 0 +s_10387 CD320 1 0 +s_64869 ZPBP 1 0 +s_54385 STK17B 1 0 +s_25423 HIST1H4D 1 0 +s_54172 ST8SIA4 9 0 +s_1161 ADCY10 1 0 +s_29184 KIAA0913 1 0 +s_42977 POLD3 1 0 +s_49449 SCUBE1 1 0 +s_24181 GRM4 1 1 +s_52507 SMARCA5 1 0 +s_28674 KCNJ10 1 0 +s_61074 VAMP2 4 0 +s_3954 ASIC2 1 0 +s_2385 ANK1 1 0 +s_18397 EPDR1 1 0 +s_18377 EPB41L4B 1 0 +s_34580 MRAP2 1 0 +s_48676 RUFY3 10 0 +s_691 ACP1 1 0 +s_30460 LAMP2 1 0 +s_42637 PLRG1 1 0 +s_12695 CNOT6 1 0 +s_33316 MECOM 2 0 +s_35081 MSRB2 1 0 +s_58512 TPD52L2 1 0 +s_19912 FAM22F 1 0 +s_45517 QSOX2 1 0 +s_56705 TINAG 1 0 +s_10946 CDKL5 1 0 +s_57473 TMEM211 2 0 +s_57657 TMEM44 1 0 +s_43200 POT1 1 0 +s_19436 FAM135A 1 0 +s_184 ABCB9 1 0 +s_30171 KRT84 1 0 +s_44758 PSMC3IP 1 0 +s_48313 RPS3 1 0 +s_58142 TNFSF12 6 0 +s_59718 TTLL6 7 0 +s_9725 CCDC43 1 0 +s_5135 BCKDHA 1 0 +s_36539 NDUFC2 1 0 +s_27251 IL27RA 1 0 +s_48939 SAMD10 1 0 +s_27343 IL5RA 1 0 +s_28386 KANK2 1 0 +s_27610 INSRR 1 0 +s_2769 AOC3 2 0 +s_58632 TRA2B 12 0 +s_6674 C16orf86 1 0 +s_22902 GJD4 1 0 +s_48278 RPS15A 1 0 +s_61998 WIPF2 1 0 +s_4937 BAIAP3 2 0 +s_54471 STOML1 2 1 +s_19157 FABP12 1 0 +s_5434 BIN1 2 0 +s_42042 PIP5K1A 1 0 +s_7794 C3orf18 1 0 +s_54846 SVIL 1 0 +s_62273 XPA 1 0 +s_45859 RACGAP1 1 0 +s_53626 SPOCK3 1 0 +s_43295 PPAP2C 7 0 +s_11788 CHRDL1 2 0 +s_50636 SHQ1 1 0 +s_16705 DPF1 1 0 +s_39741 OTOF 1 0 +s_27505 INHBE 1 0 +s_707 ACPL2 1 0 +s_15418 DDX3Y 6 0 +s_56018 TEAD4 1 0 +s_44367 PRR12 1 0 +s_25875 HOXB5 1 0 +s_49360 SCN9A 1 0 +s_16244 DMPK 1 0 +s_3909 ASCC2 1 0 +s_55088 SYT6 1 1 +s_54311 STAU1 1 0 +s_53890 SRP72 1 0 +s_11035 CDX1 1 0 +s_18178 EMR3 2 0 +s_16084 DLD 1 0 +s_47207 RHOBTB1 1 0 +s_40267 PARK2 6 0 +s_43104 POLR3B 1 0 +s_2200 AMDHD2 1 0 +s_12738 CNRIP1 1 0 +s_17842 EIF4A3 1 0 +s_57950 TMPRSS3 1 0 +s_62146 WRN 1 0 +s_11055 CEACAM1 1 0 +s_54580 STX2 1 0 +s_29277 KIAA1407 1 0 +s_33428 MEF2A 1 0 +s_59797 TUBB 1 0 +s_18113 EME1 1 1 +s_29839 KLHL8 1 0 +s_18058 ELP2 1 0 +s_49497 SDCBP2 3 0 +s_16874 DRP2 1 0 +s_13572 CREBL2 1 0 +s_20540 FBXO30 1 0 +s_64380 ZNF646 1 0 +s_50366 SH2B1 1 0 +s_2548 ANKRD33B 1 0 +s_41183 PDXP 1 1 +s_16315 DNAH12 1 0 +s_19996 FAM49B 1 0 +s_30751 LDLRAD3 1 0 +s_36960 NGEF 1 0 +s_39015 OR2A2 1 0 +s_26302 HSPB2 1 0 +s_64297 ZNF611 5 0 +s_730 ACSBG1 1 0 +s_50271 SFXN4 1 0 +s_8592 CA6 2 0 +s_13683 CRMP1 1 0 +s_51103 SLC16A7 1 0 +s_63785 ZNF384 1 0 +s_16339 DNAH9 1 0 +s_55936 TCTEX1D1 1 0 +s_14497 CXorf40A 1 0 +s_1123 ADAT1 1 0 +s_41304 PERP 1 0 +s_18719 ESAM 1 0 +s_35118 MSX2 1 0 +s_30128 KRT6A 1 0 +s_402 ABTB1 1 0 +s_32578 MAP1LC3A 1 0 +s_45063 PTMA 1 2 +s_43551 PPP1R14D 1 0 +s_2538 ANKRD32 1 0 +s_40384 PAX1 1 0 +s_29076 KIAA0101 1 0 +s_40482 PCDH10 1 0 +s_2348 ANGPT2 1 0 +s_59756 TTYH3 1 0 +s_34330 MOB4 1 0 +s_49331 SCN2B 1 0 +s_54905 SYDE1 1 0 +s_39101 OR2T1 1 0 +s_36623 NEDD4L 1 0 +s_40500 PCDH15 2 2 +s_10660 CDC42SE2 1 0 +s_30867 LGALS13 1 0 +s_24322 GSTK1 2 0 +s_59167 TRPC1 1 0 +s_57440 TMEM201 1 0 +s_50539 SHC1 1 0 +s_37087 NIT1 1 0 +s_56345 TGFB2 1 1 +s_55388 TARM1 1 0 +s_1224 ADD2 1 0 +s_5256 BCOR 2 0 +s_51731 SLC35B3 1 1 +s_12987 COL6A6 1 1 +s_56745 TJP3 1 0 +s_19340 FAM120AOS 1 0 +s_53904 SRPR 1 0 +s_1588 AGXT 1 0 +s_46157 RASA3 1 0 +s_19166 FABP3 7 0 +s_22330 GATM 1 0 +s_10731 CDH13 1 0 +s_2329 ANAPC5 1 0 +s_46045 RANGAP1 1 0 +s_54814 SUV39H2 1 0 +s_56169 TEX14 1 0 +s_3433 ARHGEF26 1 0 +s_48032 RP4-811H24.6 1 0 +s_51930 SLC41A3 1 0 +s_63893 ZNF433 1 1 +s_46996 RGCC 1 0 +s_13863 CSF3R 1 0 +s_26337 HSPH1 1 0 +s_12983 COL6A3 1 0 +s_1376 ADSS 1 0 +s_45449 PYHIN1 1 0 +s_49629 SEC22C 1 0 +s_20204 FAM86A 1 0 +s_24920 HDAC9 1 0 +s_14961 DAPK1 1 1 +s_23900 GPR98 2 0 +s_14485 CXorf27 1 0 +s_61808 WDR66 1 2 +s_55855 TCF7 1 0 +s_44652 PSG8 1 0 +s_46608 RCCD1 1 0 +s_61175 VCAM1 1 0 +s_27453 INCA1 1 0 +s_28987 KDM4C 1 0 +s_20613 FBXO7 1 0 +s_7715 C2orf70 3 1 +s_3902 ASB9 1 0 +s_64098 ZNF534 1 0 +s_31108 LIN7B 1 0 +s_3383 ARHGEF1 1 0 +s_7626 C2orf43 1 0 +s_52247 SLC8A1 1 0 +s_54498 STOX1 1 0 +s_12160 CLDN17 1 0 +s_16224 DMD 1 0 +s_41715 PHLDB2 1 0 +s_12197 CLDN7 1 0 +s_51239 SLC22A16 1 0 +s_41286 PEPD 1 0 +s_2367 ANGPTL4 1 0 +s_59289 TSC22D4 1 0 +s_22437 GCFC2 1 0 +s_24343 GSTO2 1 0 +s_32783 MAPKAPK5 1 0 +s_37032 NINJ1 1 0 +s_49065 SASH3 1 0 +s_60466 UGT1A1 1 0 +s_26043 HPSE2 2 0 +s_21199 FLNA 1 0 +s_41054 PDGFRA 1 0 +s_1820 AKNA 1 0 +s_19548 FAM166A 1 0 +s_43967 PRDX5 1 0 +s_51905 SLC39A8 1 0 +s_22723 GGT5 5 0 +s_13242 COX6C 1 0 +s_27668 IP6K1 1 0 +s_64491 ZNF692 1 0 +s_61982 WHSC1L1 2 0 +s_48495 RSAD1 1 0 +s_34351 MOCS3 1 0 +s_12069 CLCA1 3 0 +s_22023 GABRR1 1 0 +s_12812 COASY 2 0 +s_40068 PAIP1 1 0 +s_11513 CGREF1 2 0 +s_32119 LY6K 1 0 +s_60743 UQCR11 1 0 +s_56354 TGFBR1 1 0 +s_3062 APOL2 1 0 +s_20525 FBXO25 1 0 +s_55591 TBC1D7 1 0 +s_14987 DARS2 1 0 +s_63195 ZMAT2 1 0 +s_41936 PIK3C2G 1 0 +s_56092 TEP1 1 0 +s_61284 VIT 1 1 +s_10035 CCND2 1 0 +s_43744 PPP6R3 2 1 +s_48110 RPL10L 1 0 +s_39381 OR5H15 1 0 +s_6827 C17orf90 2 0 +s_8795 CADPS 1 1 +s_55301 TAF9 1 0 +s_25756 HNRNPM 1 0 +s_61177 VCAN 1 0 +s_22932 GLB1 1 0 +s_55751 TCEA2 1 0 +s_39419 OR5T3 1 0 +s_33669 MEX3A 1 0 +s_42714 PLXNC1 1 0 +s_23239 GNAT1 1 0 +s_4546 ATPAF1 1 0 +s_64432 ZNF671 1 0 +s_31346 LOXHD1 1 0 +s_46353 RBFOX2 1 0 +s_8848 CALHM2 1 0 +s_27039 IL12RB1 1 0 +s_62824 ZCCHC9 1 0 +s_7498 C20orf96 1 1 +s_43406 PPIE 1 0 +s_54925 SYN1 1 2 +s_27284 IL31RA 1 0 +s_63774 ZNF37A 1 0 +s_43643 PPP1R8 1 0 +s_63149 ZIC2 1 0 +s_26251 HSP90AB1 1 0 +s_46773 RELL2 1 0 +s_64868 ZP4 1 2 +s_626 ACLY 1 0 +s_40694 PCED1A 1 0 +s_15888 DHTKD1 1 0 +s_53641 SPP1 1 1 +s_21822 FXR1 1 0 +s_53660 SPR 1 0 +s_29906 KLKB1 1 0 +s_1901 ALAS2 1 0 +s_45130 PTPN2 1 0 +s_43535 PPP1R13B 2 0 +s_15855 DHRS12 1 0 +s_13602 CRH 1 0 +s_51848 SLC39A1 1 0 +s_61205 VDR 1 0 +s_18989 EXOC7 1 0 +s_22294 GATA1 2 0 +s_34584 MRAS 1 0 +s_33140 MCFD2 1 0 +s_34546 MPST 1 0 +s_27208 IL21R 1 0 +s_14576 CYB5R4 1 0 +s_43745 PPP6R3 1 0 +s_41675 PHF8 1 0 +s_41243 PEBP4 2 0 +s_42685 PLXNA1 1 0 +s_41585 PHB2 1 0 +s_47989 RP1L1 1 0 +s_42300 PLA2G6 1 0 +s_53387 SPATA6L 1 1 +s_15423 DDX4 1 0 +s_64039 ZNF506 5 0 +s_22276 GAS6 1 0 +s_15373 DDX19B 1 0 +s_4322 ATP2B2 1 0 +s_25787 HOMER1 1 0 +s_10739 CDH16 1 0 +s_51702 SLC34A3 1 2 +s_20623 FBXO9 2 0 +s_13244 COX6C 1 0 +s_35367 MTX2 1 0 +s_5681 BPIFB6 1 0 +s_57337 TMEM176A 1 0 +s_43464 PPM1F 1 0 +s_20530 FBXO28 1 1 +s_55958 TDGF1 1 0 +s_4516 ATP7B 1 1 +s_19128 F8 1 0 +s_40084 PAK1IP1 1 0 +s_29430 KIF20B 1 0 +s_14773 CYP46A1 1 0 +s_19102 F2R 1 0 +s_29306 KIAA1524 2 0 +s_11438 CETN3 1 1 +s_49647 SEC24D 1 0 +s_35891 NAA11 1 0 +s_10770 CDH23 2 1 +s_44838 PSMG2 1 0 +s_22687 GGCT 1 0 +s_14266 CTSW 1 0 +s_38451 NXF3 1 0 +s_60012 TYRP1 1 0 +s_13190 COTL1 1 0 +s_4721 AZI2 1 0 +s_28800 KCNMB3 1 0 +s_23136 GM2A 1 0 +s_31806 LRRC71 1 0 +s_11862 CHRNG 2 0 +s_52893 SNX12 1 0 +s_31960 LSM5 1 0 +s_3273 ARHGAP22 1 0 +s_22140 GALNT2 1 1 +s_36663 NEK1 1 0 +s_45974 RALB 1 0 +s_48582 RTCA 1 0 +s_27173 IL1RL1 1 0 +s_49800 SEMA6D 1 0 +s_18249 ENOPH1 1 0 +s_31609 LRRC10B 1 0 +s_6450 C14orf176 1 0 +s_42314 PLAC1L 1 0 +s_7822 C3orf27 1 0 +s_43695 PPP2R5C 1 0 +s_8939 CAMKV 1 0 +s_58681 TRAF7 1 0 +s_12850 COG6 1 0 +s_20936 FGF3 1 0 +s_10862 CDK17 1 0 +s_60046 UAP1 1 0 +s_42295 PLA2G5 1 0 +s_52045 SLC4A9 1 0 +s_18532 EPS8L3 1 0 +s_15737 DFNB31 1 0 +s_12691 CNOT4 1 0 +s_27651 INTS7 1 0 +s_52454 SLX4 1 0 +s_5507 BMF 1 0 +s_57583 TMEM25 1 0 +s_36267 NCK2 1 0 +s_15361 DDX17 1 0 +s_24303 GSS 1 0 +s_11095 CEBPB 2 0 +s_59318 TSG101 1 0 +s_35897 NAA16 1 1 +s_11714 CHMP3 1 0 +s_7217 C1orf186 1 0 +s_14282 CTU1 1 0 +s_53137 SOX15 1 0 +s_30977 LHX3 1 0 +s_825 ACTL6A 1 0 +s_33214 MCOLN3 1 0 +s_57706 TMEM55B 1 0 +s_41619 PHF12 1 0 +s_13595 CREM 1 0 +s_30523 LARP4 1 0 +s_6229 C11orf68 1 0 +s_17880 EIF4G2 1 0 +s_36676 NEK3 1 0 +s_23667 GPR123 1 0 +s_1296 ADORA1 1 0 +s_18235 ENHO 1 0 +s_20589 FBXO45 1 0 +s_31341 LOX 1 0 +s_20983 FGFR2 1 0 +s_44192 PRLR 1 0 +s_62014 WIPI2 1 0 +s_2585 ANKRD45 1 0 +s_14161 CTLA4 1 0 +s_63079 ZFYVE1 1 0 +s_7088 C1orf106 1 0 +s_10461 CD55 1 0 +s_24803 HBM 1 0 +s_52929 SNX21 1 0 +s_40041 PAFAH2 1 0 +s_17056 DUSP15 1 0 +s_61656 WDR12 1 0 +s_28830 KCNQ3 2 0 +s_44745 PSMB9 1 0 +s_16151 DLGAP5 1 1 +s_17799 EIF2S3 1 0 +s_49444 SCTR 1 0 +s_37203 NLGN3 1 0 +s_63798 ZNF385D 1 1 +s_42282 PLA2G4D 1 0 +s_27383 ILF3 1 0 +s_40974 PDE4DIP 1 0 +s_55037 SYT1 1 0 +s_52560 SMC6 1 0 +s_56910 TM9SF2 1 0 +s_64839 ZNHIT6 2 0 +s_20818 FES 1 0 +s_16789 DPY19L3 1 0 +s_46072 RAP2A 1 0 +s_24369 GTDC1 1 0 +s_5332 BEST3 1 0 +s_15793 DGKG 2 0 +s_13197 COX11 1 0 +s_1613 AHCYL1 1 0 +s_62445 YLPM1 1 0 +s_5441 BIN3 1 0 +s_20572 FBXO41 1 0 +s_26507 IBSP 1 0 +s_17166 DYNC2H1 1 0 +s_37694 NPNT 1 0 +s_62561 ZBP1 1 0 +s_28074 ITGB3BP 1 0 +s_13046 COMMD4 1 0 +s_4936 BAIAP3 1 0 +s_16345 DNAI1 2 1 +s_60141 UBE2D4 1 0 +s_34569 MPZL3 1 0 +s_35839 MYRIP 1 0 +s_42840 PNN 1 0 +s_64147 ZNF558 1 1 +s_21759 FUCA2 1 0 +s_62347 XYLB 1 0 +s_41049 PDGFD 1 0 +s_19760 FAM198B 1 0 +s_4944 BAMBI 1 0 +s_59471 TSSC1 1 0 +s_60224 UBE2T 1 0 +s_62753 ZC3H6 1 0 +s_29129 KIAA0355 1 0 +s_43266 PPA2 1 0 +s_48165 RPL31 1 1 +s_25918 HOXC8 1 0 +s_61309 VMO1 1 0 +s_29649 KLF5 1 0 +s_3093 APP 1 0 +s_59201 TRPM2 2 0 +s_31154 LIPH 1 0 +s_43571 PPP1R17 1 0 +s_58112 TNFRSF25 1 0 +s_22767 GHRL 1 0 +s_59817 TUBB6 1 0 +s_63192 ZMAT1 1 0 +s_7306 C1orf49 1 0 +s_37585 NOX5 1 0 +s_57817 TMEM87B 1 0 +s_3667 ARNTL2 1 0 +s_14264 CTSS 1 0 +s_61283 VIT 1 0 +s_35482 MXD3 2 0 +s_54197 STAC2 1 0 +s_54806 SUSD5 1 0 +s_22238 GAPT 1 0 +s_62113 WNT8A 1 0 +s_54543 STRN4 1 0 +s_33235 MDC1 1 0 +s_63489 ZNF224 1 0 +s_37914 NRG1 1 1 +s_36452 NDUFA3 1 0 +s_12262 CLEC3B 1 0 +s_25 AAAS 1 0 +s_50339 SGPP2 1 0 +s_30706 LDB1 1 0 +s_49357 SCN8A 1 0 +s_33618 METTL21D 1 0 +s_4402 ATP5O 1 0 +s_55017 SYNRG 1 0 +s_51299 SLC23A3 1 0 +s_34572 MR1 2 0 +s_49259 SCGB3A1 1 0 +s_17794 EIF2S1 1 0 +s_47977 RP11-744I24.1 1 0 +s_32701 MAP7 1 0 +s_32432 MAGI3 1 0 +s_36564 NDUFS6 1 0 +s_11527 CHAC1 1 0 +s_56181 TEX22 1 0 +s_714 ACPT 1 0 +s_51144 SLC18A1 1 0 +s_57122 TMEM117 1 0 +s_28872 KCTD1 1 0 +s_63600 ZNF28 1 0 +s_57369 TMEM182 1 0 +s_60388 UCK1 1 0 +s_47188 RHEB 1 0 +s_15237 DCTD 1 0 +s_42694 PLXNA4 1 0 +s_19680 FAM187B 1 0 +s_35378 MUC1 1 0 +s_38682 OGG1 1 0 +s_1085 ADAMTS9 1 0 +s_40910 PDE1A 1 0 +s_27956 ISOC2 1 0 +s_27821 IRAK1 1 0 +s_16210 DMBT1 1 1 +s_63398 ZNF184 1 0 +s_18679 ERMP1 1 0 +s_9161 CASC1 2 0 +s_45196 PTPRF 1 0 +s_23002 GLIS2 1 0 +s_17310 EBP 1 0 +s_54797 SUSD3 1 0 +s_1528 AGPAT4 1 0 +s_7045 C1QTNF6 1 0 +s_22952 GLCE 1 0 +s_7105 C1orf111 1 0 +s_36537 NDUFC1 1 0 +s_15359 DDX11 1 1 +s_32881 MARK3 1 0 +s_27486 INHA 1 0 +s_2399 ANK2 1 0 +s_60825 USP10 1 0 +s_20838 FEZ2 1 0 +s_43974 PREB 1 0 +s_16482 DNAJC5G 1 0 +s_26334 HSPG2 1 0 +s_46175 RASD1 1 0 +s_26764 IFT20 1 0 +s_14739 CYP2J2 1 0 +s_11386 CERS2 1 0 +s_5964 BTN1A1 1 0 +s_16810 DPYSL3 1 0 +s_16136 DLGAP2 1 0 +s_13401 CPPED1 1 0 +s_22359 GBGT1 1 0 +s_49575 SDSL 1 0 +s_62067 WNT16 1 1 +s_61863 WDR83OS 1 0 +s_44742 PSMB8 2 0 +s_31855 LRRFIP2 1 0 +s_528 ACADM 1 0 +s_13073 COPA 1 0 +s_32741 MAPK3 1 0 +s_38779 OPA3 1 0 +s_34827 MRPS17 1 0 +s_16969 DTX1 1 0 +s_56448 THAP4 1 0 +s_906 ACVR2A 1 0 +s_45078 PTP4A2 1 0 +s_23628 GPR101 1 0 +s_58510 TPD52L1 1 0 +s_561 ACAT2 1 0 +s_52492 SMAP2 1 0 +s_24039 GRB2 1 0 +s_46264 RASSF4 1 0 +s_39609 ORMDL3 1 0 +s_47343 RIMS4 1 0 +s_56575 THUMPD1 1 0 +s_3261 ARHGAP18 1 0 +s_8148 C6orf165 1 0 +s_17030 DUSP10 1 1 +s_56155 TEX101 1 0 +s_21191 FLI1 1 0 +s_50732 SIK1 1 0 +s_2914 APCDD1 1 0 +s_30717 LDB3 1 0 +s_4702 AXIN1 2 0 +s_21360 FNIP2 1 0 +s_54350 STEAP4 1 0 +s_57227 TMEM14A 2 0 +s_58177 TNIK 1 0 +s_7465 C20orf26 2 0 +s_17327 ECE2 1 0 +s_51639 SLC30A10 1 0 +s_4352 ATP5A1 1 0 +s_18616 ERCC8 1 0 +s_44043 PRIMA1 1 0 +s_36712 NELL2 1 0 +s_61348 VPS16 1 1 +s_2680 ANO4 1 0 +s_30437 LAMB2 1 0 +s_33742 MFSD12 1 0 +s_58796 TRHR 1 0 +s_52365 SLCO5A1 1 0 +s_41281 PEMT 1 0 +s_23427 GON4L 1 0 +s_13427 CPSF3L 1 0 +s_40193 PAPD7 1 0 +s_21543 FPGT 2 0 +s_16722 DPH2 1 0 +s_40078 PAIP2B 1 1 +s_60284 UBL5 1 0 +s_59936 TXNDC15 1 0 +s_31898 LRRTM4 1 0 +s_44833 PSMG1 2 1 +s_19552 FAM166B 1 0 +s_19478 FAM151A 1 0 +s_30185 KRTAP1-3 1 0 +s_61742 WDR45 1 0 +s_7252 C1orf212 1 0 +s_29507 KIF9 1 0 +s_2786 AP1G1 1 0 +s_21222 FLT1 1 0 +s_38408 NUP93 1 1 +s_60875 USP25 1 0 +s_39905 P2RX5 1 0 +s_54470 STOML1 1 0 +s_19064 EYA4 1 0 +s_41060 PDGFRL 1 0 +s_32049 LUC7L 1 0 +s_11837 CHRNA9 1 0 +s_64166 ZNF563 1 0 +s_11211 CENPK 1 0 +s_63097 ZFYVE21 1 0 +s_24757 HAUS4 1 0 +s_4190 ATG7 1 1 +s_48629 RTN4 1 0 +s_22880 GJB3 1 0 +s_44427 PRR7 1 0 +s_464 AC069154.2 1 0 +s_22093 GALC 1 0 +s_55367 TAPBP 1 0 +s_56672 TIMM22 1 0 +s_22286 GAS7 1 0 +s_45341 PVR 1 0 +s_34498 MPL 1 0 +s_60077 UBA7 3 0 +s_44215 PRMT5 1 0 +s_15576 DEFB125 1 0 +s_44098 PRKAR2B 3 0 +s_38270 NUDT19 1 0 +s_12662 CNNM3 1 0 +s_51149 SLC18A2 1 0 +s_42223 PKP4 1 0 +s_31072 LIMK1 1 0 +s_6339 C12orf53 1 0 +s_26400 HTR3E 1 0 +s_43315 PPARD 1 0 +s_28264 JAM3 1 0 +s_33927 MIER1 1 0 +s_11251 CEP104 1 0 +s_33388 MED24 1 0 +s_53844 SRGAP1 1 0 +s_40003 PACSIN2 1 0 +s_5428 BIK 1 0 +s_28459 KAZN 1 0 +s_12578 CNBP 1 0 +s_20731 FCRL3 1 0 +s_41692 PHKB 3 0 +s_13730 CRTC2 1 1 +s_50741 SIKE1 2 0 +s_10340 CD276 1 0 +s_42441 PLD6 1 0 +s_32600 MAP2K1 2 0 +s_21836 FXYD3 5 2 +s_33227 MCTP2 1 0 +s_23930 GPS1 1 0 +s_58948 TRIM46 1 0 +s_23579 GPER 1 0 +s_19158 FABP12 1 0 +s_26003 HPGD 1 0 +s_12701 CNOT7 1 0 +s_41164 PDS5B 1 0 +s_35675 MYLIP 1 0 +s_54071 SSX5 1 0 +s_59652 TTC9C 1 0 +s_35593 MYH10 1 0 +s_28060 ITGB1BP1 1 0 +s_52258 SLC8A3 2 0 +s_52898 SNX14 1 0 +s_25618 HMGCS1 1 0 +s_5068 BBS9 1 0 +s_4389 ATP5J 1 1 +s_49674 SEC62 1 0 +s_10264 CD1D 1 0 +s_20442 FBXL16 1 0 +s_11296 CEP41 1 0 +s_64923 ZSCAN22 1 0 +s_43954 PRDX3 1 1 +s_41735 PHOX2A 1 0 +s_33740 MFSD11 1 0 +s_2779 AP000892.1 1 0 +s_12703 CNOT7 1 0 +s_23338 GNMT 1 0 +s_14454 CXXC1 1 0 +s_49387 SCO1 1 0 +s_9124 CARD8 1 0 +s_42754 PML 2 4 +s_38814 OPRD1 1 0 +s_40024 PADI4 1 0 +s_29225 KIAA1147 1 0 +s_43402 PPID 1 0 +s_58669 TRAF3IP3 1 0 +s_59528 TTC17 1 0 +s_19114 F2RL3 1 0 +s_3339 ARHGAP35 1 0 +s_1522 AGPAT2 1 0 +s_33006 MBD2 1 0 +s_64149 ZNF558 1 0 +s_9791 CCDC69 1 0 +s_51442 SLC25A4 1 0 +s_59174 TRPC4 1 0 +s_37772 NQO2 1 0 +s_28649 KCNH8 1 0 +s_39896 P2RX3 1 0 +s_44644 PSG4 1 0 +s_51440 SLC25A39 1 0 +s_23954 GPSM3 1 0 +s_58911 TRIM36 1 0 +s_20632 FBXW12 1 0 +s_50149 SETMAR 1 0 +s_42606 PLK4 2 0 +s_55148 TAB1 1 0 +s_64628 ZNF772 1 0 +s_10616 CDC34 1 0 +s_38307 NUDT8 1 0 +s_23831 GPR35 1 0 +s_17055 DUSP15 1 0 +s_6922 C19orf44 1 0 +s_42494 PLEKHF2 1 0 +s_2104 ALPK1 1 0 +s_17640 EGFR 1 0 +s_37797 NR1H3 1 0 +s_23299 GNG3 1 0 +s_9517 CCDC125 1 0 +s_7562 C22orf42 1 0 +s_38149 NTNG1 1 0 +s_64633 ZNF774 1 0 +s_34420 MORN3 1 0 +s_56144 TET2 1 0 +s_18093 EMC6 1 0 +s_63835 ZNF410 1 0 +s_35521 MYBPC1 1 0 +s_64601 ZNF75D 1 0 +s_42105 PITX2 1 1 +s_39091 OR2M4 2 0 +s_1765 AKAP13 1 0 +s_6189 C11orf45 1 0 +s_63701 ZNF330 1 0 +s_28136 ITM2A 1 0 +s_56984 TMCO1 1 0 +s_49007 SAMSN1 1 0 +s_33654 METTL7A 2 0 +s_41626 PHF14 1 0 +s_34072 MLF1 1 0 +s_8880 CALR 1 0 +s_8738 CACNB4 1 0 +s_64012 ZNF496 1 0 +s_59206 TRPM3 1 0 +s_3971 ASIC5 1 0 +s_190 ABCC10 1 0 +s_41999 PIM1 1 1 +s_64465 ZNF684 1 0 +s_18728 ESD 1 0 +s_33786 MGA 1 0 +s_39611 OS9 1 0 +s_3484 ARID1B 1 0 +s_1238 ADH4 1 0 +s_53695 SPRTN 1 0 +s_23676 GPR126 1 0 +s_26052 HRAS 1 0 +s_36545 NDUFS1 1 0 +s_63208 ZMAT5 1 0 +s_2908 APC 1 0 +s_15119 DCAF8 1 0 +s_64395 ZNF655 1 0 +s_54556 STUB1 1 0 +s_10027 CCNC 1 0 +s_20178 FAM83C 1 0 +s_38266 NUDT17 1 1 +s_63517 ZNF233 1 0 +s_5435 BIN1 3 0 +s_13322 CPEB3 3 0 +s_19210 FAHD2A 1 0 +s_28276 JDP2 1 0 +s_38449 NXF1 1 0 +s_44619 PSEN1 1 0 +s_49290 SCMH1 1 0 +s_63232 ZMYM3 1 0 +s_47908 RP11-173D9.3 1 0 +s_51358 SLC25A18 1 0 +s_42513 PLEKHG5 1 0 +s_270 ABHD1 1 0 +s_58611 TPSG1 1 0 +s_45665 RAB33A 1 0 +s_35550 MYCL1 1 0 +s_55953 TCTN3 1 0 +s_39190 OR4D5 1 0 +s_64862 ZP2 1 0 +s_48451 RRM2 1 0 +s_44136 PRKCZ 1 0 +s_12532 CMTM1 1 0 +s_13958 CSPP1 1 0 +s_61437 VSIG1 1 0 +s_2427 ANKH 1 0 +s_48236 RPP25 1 0 +s_25248 HHIP 1 0 +s_49666 SEC61A2 2 0 +s_40916 PDE1C 1 0 +s_51267 SLC22A3 2 0 +s_45250 PTPRU 1 0 +s_54454 STMN2 1 0 +s_50448 SH3BP5 1 0 +s_35505 MYB 1 0 +s_34174 MMD2 1 0 +s_43046 POLR1D 1 0 +s_26919 IGSF1 1 0 +s_59350 TSKU 1 0 +s_52462 SMAD3 1 0 +s_44496 PRSS22 1 0 +s_12310 CLIC1 1 0 +s_60920 USP38 1 0 +s_42557 PLEKHO2 1 0 +s_37636 NPEPL1 1 0 +s_56222 TFAP2A 1 1 +s_46417 RBM22 1 0 +s_20477 FBXL6 1 0 +s_30504 LAPTM4A 1 0 +s_49873 4-Sep 1 0 +s_22231 GAPDH 1 0 +s_24866 HCRT 1 0 +s_26084 HRH4 1 0 +s_266 ABCG8 1 0 +s_31387 LPCAT1 1 0 +s_38114 NTF3 1 0 +s_13990 CST11 1 0 +s_24036 GRB14 1 0 +s_50585 SHISA4 1 0 +s_14163 CTNNA1 1 0 +s_1729 AK2 1 0 +s_62985 ZFHX3 1 0 +s_21318 FNBP1L 1 0 +s_13575 CREBRF 1 1 +s_5344 BET1 1 0 +s_49424 SCRN2 1 0 +s_31170 LIPN 1 0 +s_54781 SURF2 1 0 +s_51325 SLC25A1 1 0 +s_34136 MLNR 1 0 +s_31677 LRRC31 1 0 +s_53307 SPARCL1 1 0 +s_28022 ITGA7 1 0 +s_31356 LOXL3 1 0 +s_118 ABCA12 1 0 +s_12481 CLUL1 1 0 +s_40393 PAX3 1 0 +s_39614 OS9 1 0 +s_22342 GBA2 1 0 +s_1136 ADC 1 0 +s_10401 CD37 1 0 +s_4512 ATP7A 1 0 +s_10615 CDC27 1 0 +s_54497 STOX1 1 0 +s_46754 REG4 1 0 +s_20299 FAP 1 0 +s_63316 ZNF138 1 0 +s_42213 PKP2 1 0 +s_52161 SLC6A4 1 0 +s_60954 USP48 1 0 +s_14721 CYP2C9 1 0 +s_54067 SSX3 1 0 +s_42512 PLEKHG5 1 0 +s_32324 MAD2L1BP 1 0 +s_26149 HSD11B1L 1 1 +s_62941 ZFAND1 1 0 +s_306 ABHD16A 1 0 +s_42173 PKIG 1 0 +s_33499 MEOX1 1 1 +s_2639 ANKS1A 1 0 +s_9221 CASP4 2 2 +s_60951 USP48 1 0 +s_42487 PLEKHB2 1 0 +s_12463 CLTB 1 0 +s_17140 DYDC2 1 0 +s_15238 DCTD 1 0 +s_32766 MAPK8IP3 1 0 +s_6844 C18orf1 1 0 +s_29768 KLHL25 1 0 +s_58192 TNIP3 1 0 +s_26239 HSF4 1 0 +s_14209 CTRL 1 0 +s_7539 C22orf25 1 0 +s_21263 FMNL3 1 0 +s_56798 TLK1 1 0 +s_30163 KRT80 1 0 +s_28530 KCNAB1 1 0 +s_50079 SESN2 1 0 +s_17622 EGFL7 1 0 +s_27107 IL17RE 1 0 +s_61128 VASH2 1 0 +s_7629 C2orf44 1 0 +s_59045 TRIML2 1 0 +s_53186 SP110 1 0 +s_44696 PSMA8 1 0 +s_4081 ATAT1 1 0 +s_59776 TUBA3C 1 0 +s_26981 IKBKB 1 0 +s_11984 CINP 1 0 +s_38231 NUDT1 1 0 +s_34096 MLKL 1 0 +s_39703 OSM 1 0 +s_44761 PSMC4 1 0 +s_29844 KLK1 1 0 +s_46470 RBM43 1 0 +s_21735 FTSJ1 1 0 +s_54159 ST7L 1 0 +s_29161 KIAA0586 1 0 +s_62066 WNT11 1 0 +s_32768 MAPK9 1 0 +s_38834 OPTC 1 0 +s_27041 IL12RB2 1 0 +s_25301 HIGD1C 1 0 +s_48626 RTN4 1 0 +s_2191 AMBRA1 1 0 +s_64637 ZNF775 1 0 +s_24425 GTF2IRD1 2 0 +s_28025 ITGA7 1 0 +s_21739 FTSJ2 1 0 +s_56140 TET1 1 0 +s_18340 EOGT 1 0 +s_48335 RPS6KA1 1 0 +s_8918 CAMK2N1 1 1 +s_9126 CARD8 1 0 +s_34993 MSC 1 0 +s_62519 YY1AP1 1 0 +s_17754 EIF2B2 1 0 +s_3894 ASB7 1 0 +s_1366 ADRBK2 1 0 +s_63368 ZNF169 1 0 +s_33217 MCRS1 1 0 +s_791 ACSS3 1 0 +s_3070 APOL5 1 0 +s_158 ABCB4 1 0 +s_46169 RASAL2 1 0 +s_31573 LRP3 1 0 +s_15806 DGKQ 1 0 +s_3426 ARHGEF2 1 0 +s_22505 GDAP2 1 0 +s_43731 PPP4R4 1 0 +s_62463 YPEL3 1 1 +s_1351 ADRA2A 1 0 +s_58570 TPPP 1 0 +s_27563 INPP5K 1 0 +s_64662 ZNF783 1 0 +s_43701 PPP2R5D 1 0 +s_41032 PDE9A 1 0 +s_40077 PAIP2B 1 0 +s_55106 SYTL2 1 0 +s_36104 NAT1 1 0 +s_5659 BPIFA2 1 0 +s_24738 HAS3 1 0 +s_23688 GPR135 1 0 +s_44125 PRKCI 1 0 +s_42154 PKDCC 1 0 +s_52320 SLC9B2 1 0 +s_56287 TFF1 1 0 +s_26218 HSDL1 1 0 +s_48811 S100A14 1 0 +s_27403 IMMT 1 0 +s_44547 PRSS50 1 0 +s_13554 CREB3L3 1 0 +s_52812 SNRNP35 1 0 +s_9678 CCDC28B 1 0 +s_42982 POLD4 1 0 +s_9038 CAPN3 1 0 +s_24550 GYG1 1 1 +s_7927 C4orf19 1 0 +s_59893 TWF2 1 0 +s_21776 FUS 1 0 +s_38699 OLA1 1 0 +s_15466 DDX54 1 0 +s_57105 TMEM110 1 0 +s_47396 RIPPLY2 1 0 +s_29679 KLHDC3 1 0 +s_19864 FAM214B 1 0 +s_22859 GIT2 1 0 +s_63818 ZNF397 1 0 +s_62767 ZC3HAV1 1 0 +s_30390 LAD1 1 0 +s_54683 SULT1C3 1 0 +s_29008 KDM5D 1 0 +s_24721 HARS 1 0 +s_19875 FAM217A 1 0 +s_33598 METTL18 1 0 +s_43299 PPAPDC1B 1 0 +s_23606 GPM6A 1 0 +s_8917 CAMK2G 1 0 +s_7803 C3orf22 1 0 +s_52734 SNAP91 2 0 +s_46558 RBPJL 1 1 +s_44462 PRRT2 1 0 +s_30938 LHB 1 0 +s_33858 MIA2 1 0 +s_1394 AEN 1 0 +s_39870 OXSR1 1 0 +s_4906 BAG6 1 0 +s_16155 DLK2 1 0 +s_35274 MTMR4 1 0 +s_10518 CD81 1 0 +s_39057 OR2F2 1 0 +s_43913 PRDM16 1 0 +s_34638 MRPL1 1 0 +s_612 ACER3 1 0 +s_32740 MAPK3 1 0 +s_16130 DLGAP1 1 1 +s_15564 DEFB119 1 0 +s_41047 PDGFC 1 0 +s_30824 LEPRE1 1 0 +s_19702 FAM189B 1 0 +s_16740 DPM3 1 0 +s_13557 CREB3L4 1 0 +s_10008 CCNA1 1 1 +s_58486 TP73 1 0 +s_18717 ESAM 1 0 +s_63612 ZNF280D 1 0 +s_14187 CTNND2 1 0 +s_59449 TSPO2 1 0 +s_42709 PLXNB3 1 0 +s_39221 OR4M2 1 0 +s_49750 SEMA3F 1 0 +s_8476 C9orf3 1 1 +s_45561 RAB11A 1 1 +s_5542 BMP5 1 0 +s_1064 ADAMTS4 1 0 +s_5354 BET3L 1 0 +s_17631 EGFLAM 1 0 +s_36593 NEBL 1 0 +s_6085 C10orf2 1 0 +s_13428 CPSF3L 1 0 +s_25023 HECW1 1 0 +s_3641 ARMC9 1 0 +s_56315 TFPT 1 0 +s_3278 ARHGAP22 1 0 +s_49946 SERPINA1 1 0 +s_20760 FDFT1 1 0 +s_26065 HRCT1 1 0 +s_50473 SH3GL1 1 0 +s_22971 GLI1 1 0 +s_24638 H6PD 1 0 +s_40488 PCDH11X 1 0 +s_61210 VEGFB 1 0 +s_28841 KCNQ5 1 0 +s_43717 PPP3R1 1 0 +s_25342 HIRA 1 0 +s_57951 TMPRSS4 1 0 +s_34011 MITF 1 0 +s_54412 STK32B 1 0 +s_16037 DISC1 1 0 +s_51701 SLC34A3 1 0 +s_54291 STAT4 1 0 +s_24419 GTF2I 1 0 +s_45973 RALB 1 0 +s_28705 KCNJ6 1 0 +s_5581 BNIP1 1 0 +s_19856 FAM213A 1 0 +s_18308 ENTPD1 1 0 +s_59198 TRPM1 1 0 +s_21871 FZD10 1 0 +s_1850 AKR1C4 1 0 +s_6867 C18orf54 1 0 +s_35715 MYO18B 1 0 +s_22242 GAPVD1 1 0 +s_32713 MAP7D3 1 0 +s_49953 SERPINA12 1 0 +s_55916 TCP11 1 0 +s_56174 TEX19 1 0 +s_22072 GAL 1 0 +s_41033 PDE9A 1 1 +s_26471 HYAL3 1 1 +s_60244 UBE2Z 1 0 +s_12589 CNEP1R1 1 0 +s_29896 KLK8 1 0 +s_29769 KLHL26 1 0 +s_39346 OR5AP2 1 0 +s_15213 DCPS 1 0 +s_48577 RTBDN 1 0 +s_32146 LYAR 1 0 +s_26382 HTR3C 1 0 +s_33001 MBD1 1 0 +s_41972 PIK3R2 1 0 +s_33212 MCOLN3 1 0 +s_35423 MUL1 1 0 +s_7838 C3orf35 1 0 +s_51092 SLC16A4 1 0 +s_20336 FASTK 1 0 +s_33469 MEI1 1 0 +s_5549 BMP7 1 0 +s_2490 ANKRD16 1 0 +s_38674 OGFRL1 1 0 +s_26322 HSPBAP1 1 0 +s_31244 LMNA 1 0 +s_34063 MLC1 1 0 +s_15550 DEFB113 1 0 +s_52892 SNX12 1 0 +s_25799 HOOK2 1 0 +s_55486 TAX1BP1 1 1 +s_4351 ATP5A1 1 0 +s_49917 SERHL2 1 0 +s_46614 RCHY1 1 0 +s_62680 ZBTB7B 1 0 +s_49488 SDCBP 1 0 +s_21866 FYTTD1 1 0 +s_23092 GLTPD1 1 0 +s_10675 CDC73 1 0 +s_12764 CNTN2 1 0 +s_9223 CASP5 1 1 +s_38310 NUDT8 1 0 +s_7059 C1QTNF9B 1 0 +s_33162 MCM3AP 1 0 +s_8498 C9orf50 1 0 +s_16876 DSC1 1 0 +s_14370 CWH43 1 0 +s_22565 GDPD1 1 0 +s_4304 ATP1B4 1 0 +s_3600 ARMC10 1 0 +s_18120 EMID1 1 0 +s_21865 FYN 1 0 +s_60042 U2SURP 1 0 +s_13930 CSNK1G3 1 0 +s_6618 C16orf53 1 0 +s_26173 HSD17B12 1 0 +s_46035 RANBP3L 1 0 +s_13167 CORO2A 1 0 +s_10481 CD6 1 0 +s_4563 ATPIF1 1 0 +s_50071 SERTAD4 1 0 +s_39089 OR2M3 1 0 +s_58390 TOR1AIP2 1 0 +s_45132 PTPN2 1 0 +s_34536 MPPED2 1 0 +s_24336 GSTM5 1 0 +s_38670 OGFR 1 0 +s_4606 ATXN3 1 0 +s_5049 BBS12 1 0 +s_28134 ITM2A 1 0 +s_23612 GPN1 1 0 +s_16085 DLEC1 1 0 +s_2525 ANKRD28 1 0 +s_1792 AKAP7 1 0 +s_27701 IPO11 1 0 +s_25633 HMGN5 1 0 +s_33287 MDM4 1 0 +s_17847 EIF4E 1 0 +s_58327 TOMM34 1 0 +s_54101 ST3GAL3 1 0 +s_41507 PGLYRP3 1 0 +s_38705 OLAH 1 0 +s_7336 C1orf61 1 0 +s_34439 MOSPD3 1 0 +s_33343 MED12 1 0 +s_30145 KRT75 1 0 +s_7793 C3orf18 1 0 +s_13874 CSH2 1 1 +s_14274 CTTN 1 0 +s_38166 NTRK2 1 0 +s_2916 APCDD1L 1 0 +s_41582 PHB 1 0 +s_16033 DISC1 1 0 +s_54156 ST7L 1 0 +s_21942 GABARAPL1 1 0 +s_19312 FAM115C 1 0 +s_5431 BIN1 1 0 +s_44378 PRR15 1 0 +s_22113 GALNT1 1 0 +s_11744 CHN1 1 0 +s_13702 CROT 1 0 +s_14052 CT62 1 0 +s_28143 ITM2C 1 0 +s_43456 PPM1B 1 0 +s_1396 AES 1 0 +s_21931 GAB2 1 0 +s_39536 OR8J3 1 0 +s_62622 ZBTB37 1 0 +s_10417 CD3G 1 0 +s_23789 GPR176 1 0 +s_37011 NICN1 1 0 +s_55412 TAS1R2 1 0 +s_36626 NEDD4L 1 0 +s_62812 ZCCHC4 1 0 +s_18097 EMC7 1 0 +s_36145 NAV2 1 0 +s_18994 EXOG 1 0 +s_61047 UTY 1 0 +s_57912 TMPRSS11B 1 0 +s_56577 THUMPD1 1 0 +s_8419 C9orf123 1 0 +s_36127 NAT9 1 0 +s_57557 TMEM240 1 0 +s_36157 NBEA 1 0 +s_16271 DMRTA2 1 0 +s_44643 PSG4 1 0 +s_53557 SPINK8 1 0 +s_36256 NCF4 1 0 +s_46280 RASSF6 1 0 +s_47580 RNF141 1 0 +s_8514 C9orf71 1 0 +s_62629 ZBTB4 1 0 +s_4286 ATP1A3 1 1 +s_36001 NAGK 1 0 +s_38778 OPA3 1 0 +s_8907 CAMK2A 1 0 +s_10448 CD5 1 0 +s_20085 FAM69B 1 0 +s_31389 LPCAT1 1 0 +s_56204 TEX34 1 0 +s_30139 KRT72 1 0 +s_34962 MS4A6A 1 0 +s_12886 COL17A1 1 0 +s_46458 RBM4 1 0 +s_37813 NR1I3 1 0 +s_60438 UFSP1 0 1 +s_63435 ZNF200 0 2 +s_64396 ZNF655 0 1 +s_43862 PRB4 0 1 +s_53525 SPIN1 0 1 +s_50517 SH3TC2 0 1 +s_30311 KRTAP9-3 0 1 +s_22485 GCNT2 0 1 +s_3888 ASB6 0 1 +s_40184 PAPD4 0 1 +s_32073 LUZP1 0 1 +s_6525 C15orf39 0 2 +s_23767 GPR161 0 1 +s_30263 KRTAP26-1 0 1 +s_15363 DDX17 0 1 +s_51344 SLC25A13 0 2 +s_57150 TMEM127 0 1 +s_5006 BAZ1A 0 1 +s_1035 ADAMTS14 0 1 +s_12177 CLDN2 0 1 +s_2968 APLP1 0 1 +s_27202 IL20RB 0 1 +s_31454 LPPR5 0 1 +s_56373 TGIF1 0 1 +s_38212 NUCB2 0 1 +s_35682 MYLK 0 1 +s_11692 CHL1 0 1 +s_45600 RAB15 0 1 +s_45050 PTK2 0 1 +s_43302 PPAPDC1B 0 1 +s_6106 C10orf54 0 1 +s_15965 DIAPH3 0 1 +s_40436 PBOV1 0 1 +s_18809 ETHE1 0 1 +s_19255 FAM104B 0 1 +s_12666 CNNM3 0 1 +s_24320 GSTCD 0 1 +s_53555 SPINK6 0 1 +s_15731 DFFB 0 1 +s_27958 IST1 0 1 +s_964 ADAM18 0 2 +s_53438 SPDYC 0 1 +s_45128 PTPN18 0 1 +s_39135 OR2T8 0 1 +s_16417 DNAJC13 0 1 +s_50127 SETD7 0 1 +s_47970 RP11-6F2.7 0 1 +s_29117 KIAA0284 0 1 +s_41474 PGBD2 0 1 +s_17709 EHMT2 0 1 +s_42616 PLOD1 0 2 +s_48098 RPH3AL 0 1 +s_33131 MCF2 0 1 +s_40137 PAM 0 1 +s_43789 PQLC2 0 1 +s_64930 ZSCAN30 0 1 +s_51904 SLC39A8 0 1 +s_2509 ANKRD23 0 1 +s_52206 SLC7A14 0 1 +s_29841 KLHL8 0 1 +s_41294 PER2 0 1 +s_19006 EXOSC3 0 1 +s_58256 TNPO2 0 1 +s_62361 YAE1D1 0 1 +s_41955 PIK3CD 0 1 +s_55577 TBC1D30 0 1 +s_4898 BAG4 0 1 +s_36143 NAV2 0 1 +s_40521 PCDH7 0 1 +s_38169 NTRK2 0 1 +s_18119 EMID1 0 1 +s_13067 COMT 0 1 +s_1101 ADAMTSL4 0 1 +s_43837 PRAMEF16 0 1 +s_23618 GPN3 0 1 +s_21231 FLT4 0 1 +s_32160 LYL1 0 1 +s_40510 PCDH19 0 1 +s_31587 LRP8 0 1 +s_63034 ZFP64 0 1 +s_41347 PEX19 0 1 +s_6849 C18orf21 0 1 +s_52784 SNIP1 0 1 +s_52587 SMG5 0 1 +s_27324 IL37 0 1 +s_27482 ING4 0 2 +s_44189 PRLR 0 2 +s_15655 DENND4A 0 1 +s_58962 TRIM50 0 1 +s_31344 LOXHD1 0 2 +s_9710 CCDC40 0 1 +s_8227 C7orf10 0 2 +s_51872 SLC39A14 0 1 +s_21627 FRMD8 0 1 +s_54092 ST3GAL3 0 1 +s_59160 TROVE2 0 1 +s_13091 COPG1 0 1 +s_23236 GNAS 0 1 +s_41084 PDIA4 0 1 +s_5437 BIN2 0 1 +s_10405 CD38 0 1 +s_58485 TP73 0 1 +s_26862 IGFBP5 0 1 +s_19747 FAM195B 0 1 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+s_41138 PDLIM5 0 1 +s_56167 TEX13B 0 1 +s_45707 RAB3C 0 1 +s_32418 MAGEE2 0 2 +s_14021 CSTA 0 1 +s_33218 MCRS1 0 1 +s_64627 ZNF772 0 1 +s_53535 SPINK1 0 1 +s_52617 SMO 0 1 +s_43542 PPP1R14A 0 1 +s_12120 CLCN7 0 1 +s_28288 JMJD1C 0 2 +s_14439 CXCR4 0 1 +s_52421 SLITRK4 0 1 +s_59311 TSEN54 0 1 +s_40055 PAGE2B 0 1 +s_58211 TNKS2 0 1 +s_17440 EDNRA 0 1 +s_18767 ESRRA 0 1 +s_4224 ATN1 0 1 +s_6639 C16orf62 0 1 +s_15482 DDX6 0 1 +s_47216 RHOC 0 1 +s_5618 BOK 0 1 +s_24664 HADHB 0 1 +s_3145 AQP7 0 1 +s_48066 RPAP3 0 1 +s_33750 MFSD2B 0 1 +s_55844 TCF4 0 1 +s_59859 TULP1 0 1 +s_41807 PIAS1 0 1 +s_20686 FCGR1A 0 1 +s_48512 RSC1A1 0 1 +s_17195 DYRK1B 0 1 +s_42467 PLEKHA5 0 1 +s_37430 NODAL 0 1 +s_4837 B4GALT5 0 1 +s_53055 SORBS1 0 2 +s_34503 MPND 0 1 +s_25337 HIPK4 0 2 +s_32434 MAGI3 0 1 +s_35796 MYOF 0 1 +s_8910 CAMK2B 0 1 +s_49354 SCN7A 0 1 +s_48438 RREB1 0 1 +s_1116 ADARB1 0 2 +s_41772 PHYHIPL 0 1 +s_27183 IL1RN 0 1 +s_54942 SYNDIG1 0 1 +s_21845 FXYD5 0 1 +s_64898 ZSCAN10 0 1 +s_3120 AQP10 0 3 +s_64652 ZNF780A 0 1 +s_20269 FANCC 0 1 +s_30538 LARP7 0 1 +s_58690 TRAK1 0 2 +s_64871 ZPBP 0 1 +s_32 AADACL2 0 1 +s_40016 PADI2 0 1 +s_31415 LPHN3 0 7 +s_27571 INS 0 1 +s_19605 FAM173B 0 1 +s_56415 TGS1 0 1 +s_29897 KLK8 0 1 +s_6427 C14orf133 0 3 +s_34406 MORF4L2 0 1 +s_4972 BARHL2 0 1 +s_51613 SLC2A6 0 1 +s_39500 OR7D4 0 2 +s_40004 PACSIN2 0 1 +s_49570 SDR9C7 0 1 +s_20794 FEM1C 0 1 +s_34529 MPP7 0 2 +s_33192 MCM9 0 3 +s_28004 ITGA3 0 1 +s_17432 EDN2 0 1 +s_50491 SH3KBP1 0 1 +s_15897 DHX16 0 1 +s_3297 ARHGAP26 0 2 +s_55862 TCF7L2 0 1 +s_21736 FTSJ1 0 1 +s_1834 AKR1B10 0 1 +s_28650 KCNIP1 0 1 +s_52017 SLC4A2 0 1 +s_19699 FAM189B 0 1 +s_37048 NIPA1 0 1 +s_27265 IL2RA 0 1 +s_47144 RHAG 0 1 +s_22537 GDF5 0 1 +s_27330 IL4I1 0 1 +s_9925 CCL1 0 1 +s_37151 NKX2-5 0 1 +s_35519 MYBPC1 0 1 +s_10381 CD300LG 0 1 +s_3881 ASB4 0 1 +s_62275 XPC 0 1 +s_44739 PSMB8 0 1 +s_54645 SUCNR1 0 1 +s_60169 UBE2H 0 1 +s_59332 TSHB 0 1 +s_24129 GRIN2D 0 1 +s_40487 PCDH11X 0 1 +s_59717 TTLL6 0 1 +s_19048 EXTL2 0 1 +s_16675 DOPEY1 0 1 +s_40227 PAQR5 0 1 +s_9584 CCDC149 0 1 +s_1609 AHCY 0 1 +s_57016 TMED10 0 1 +s_17959 ELF5 0 1 +s_54292 STAT5A 0 3 +s_2464 ANKRD10 0 1 +s_32012 LTBP1 0 1 +s_26858 IGFBP4 0 1 +s_10582 CDC14B 0 1 +s_5253 BCO2 0 1 +s_63746 ZNF354B 0 1 +s_52758 SNAPIN 0 1 +s_32521 MAN2B1 0 1 +s_58237 TNNT1 0 1 +s_32773 MAPKAP1 0 1 +s_42321 PLAC8L1 0 2 +s_16798 DPYD 0 2 +s_7674 C2orf57 0 1 +s_52313 SLC9B1 0 1 +s_44091 PRKAR1B 0 1 +s_58533 TPI1 0 1 +s_62257 XKR6 0 1 +s_51096 SLC16A5 0 1 +s_13856 CSF3 0 2 +s_60542 UGT3A1 0 1 +s_12121 CLCN7 0 1 +s_36740 NEU1 0 1 +s_62657 ZBTB47 0 2 +s_61173 VCAM1 0 1 +s_18908 EVL 0 1 +s_55709 TBX21 0 1 +s_19254 FAM104A 0 1 +s_32407 MAGEC3 0 1 +s_27828 IRAK2 0 1 +s_42751 PML 0 1 +s_14894 DAB2IP 0 1 +s_5588 BNIP2 0 1 +s_54054 SSTR5 0 1 +s_60209 UBE2Q2 0 2 +s_33476 MEIS2 0 1 +s_4925 BAIAP2 0 1 +s_36282 NCKAP5 0 1 +s_24146 GRIP1 0 1 +s_804 ACTB 0 1 +s_6068 C10orf125 0 1 +s_56819 TLR10 0 2 +s_12576 CNBP 0 1 +s_31007 LIAS 0 1 +s_13123 COQ2 0 1 +s_39747 OTOF 0 1 +s_61341 VPS13C 0 1 +s_61367 VPS29 0 1 +s_14189 CTNND2 0 1 +s_49859 12-Sep 0 1 +s_26290 HSPA8 0 1 +s_54866 SWT1 0 1 +s_11222 CENPM 0 1 +s_60614 UNC119 0 4 +s_14226 CTSC 0 1 +s_12187 CLDN25 0 1 +s_54684 SULT1C3 0 1 +s_3938 ASGR2 0 1 +s_53109 SOSTDC1 0 1 +s_21650 FRS3 0 1 +s_15440 DDX47 0 1 +s_29590 KLC3 0 1 +s_39262 OR51F2 0 1 +s_9868 CCDC89 0 1 +s_9064 CAPRIN1 0 1 +s_35811 MYOM3 0 2 +s_37972 NRSN2 0 1 +s_55520 TBC1D14 0 1 +s_1127 ADAT2 0 1 +s_57288 TMEM164 0 1 +s_57422 TMEM198 0 3 +s_38963 OR1A2 0 1 +s_14467 CXXC5 0 1 +s_40148 PAN2 0 1 +s_16866 DRGX 0 1 +s_61739 WDR44 0 1 +s_38225 NUDCD2 0 1 +s_40261 PARD6B 0 1 +s_52485 SMAP1 0 1 +s_48488 RRS1 0 1 +s_5974 BTN3A1 0 1 +s_40182 PAOX 0 1 +s_46581 RCAN1 0 1 +s_36044 NANS 0 1 +s_31011 LIF 0 1 +s_61640 WDHD1 0 1 +s_6814 C17orf80 0 1 +s_26557 ICT1 0 1 +s_8879 CALR 0 1 +s_18125 EMILIN1 0 1 +s_20635 FBXW2 0 1 +s_60517 UGT2A1 0 2 +s_62559 ZBED6 0 1 +s_35186 MTF1 0 1 +s_62320 XRCC4 0 1 +s_43060 POLR2C 0 1 +s_18739 ESM1 0 3 +s_35923 NAA60 0 1 +s_8930 CAMKK1 0 1 +s_13198 COX11 0 1 +s_42392 PLCH1 0 1 +s_46827 RERGL 0 1 +s_44808 PSMD8 0 1 +s_27580 INSIG1 0 1 +s_8403 C9orf100 0 1 +s_31142 LIPF 0 1 +s_37816 NR2C1 0 1 +s_64241 ZNF586 0 1 +s_4457 ATP6V0E2 0 1 +s_13486 CR2 0 1 +s_17901 EIF5A2 0 1 +s_34151 MLXIPL 0 1 +s_37810 NR1I3 0 3 +s_3141 AQP6 0 1 +s_13857 CSF3 0 1 +s_1550 AGPS 0 1 +s_51783 SLC35G2 0 1 +s_15488 DDX60L 0 1 +s_16745 DPP10 0 1 +s_44361 PRPSAP2 0 1 +s_23683 GPR132 0 1 +s_4209 ATL2 0 1 +s_3146 AQP8 0 1 +s_64581 ZNF746 0 1 +s_34918 MRVI1 0 2 +s_24916 HDAC8 0 1 +s_31550 LRP12 0 1 +s_50560 SHE 0 1 +s_50761 SIPA1 0 2 +s_43253 POU6F2 0 1 +s_1599 AGXT2L1 0 1 +s_56284 TFEC 0 1 +s_33844 MGST1 0 1 +s_12611 CNGB1 0 2 +s_38747 OLR1 0 1 +s_38825 OPRM1 0 1 +s_34294 MNT 0 2 +s_31279 LMOD1 0 1 +s_28463 KAZN 0 1 +s_7341 C1orf63 0 1 +s_3544 ARL16 0 1 +s_42148 PKD2L2 0 1 +s_35281 MTMR7 0 1 +s_35008 MSH4 0 1 +s_441 AC013461.1 0 1 +s_37222 NLRC4 0 1 +s_20946 FGF5 0 1 +s_21281 FMO4 0 1 +s_42351 PLB1 0 1 +s_3841 ASB11 0 1 +s_63935 ZNF446 0 1 +s_44726 PSMB5 0 1 +s_18567 ERBB2IP 0 1 +s_4507 ATP6V1H 0 1 +s_3526 ARL11 0 1 +s_60851 USP19 0 1 +s_11585 CHD1 0 1 +s_15648 DENND2D 0 1 +s_64393 ZNF655 0 1 +s_15052 DBP 0 1 +s_37438 NOL10 0 1 +s_59955 TXNDC8 0 1 +s_32844 6-Mar 0 1 +s_46107 RAPH1 0 1 +s_13579 CREBZF 0 1 +s_56006 TEAD2 0 1 +s_32687 MAP6 0 1 +s_893 ACVR1B 0 1 +s_59360 TSNARE1 0 1 +s_19664 FAM183A 0 1 +s_34715 MRPL33 0 1 +s_46646 RD3 0 1 +s_37579 NOX4 0 1 +s_58809 TRIB2 0 1 +s_62624 ZBTB37 0 1 +s_57700 TMEM54 0 1 +s_1113 ADAR 0 1 +s_14938 DALRD3 0 1 +s_39650 OSBPL3 0 1 +s_53574 SPINT1 0 1 +s_36335 NCR1 0 1 +s_54772 SUPV3L1 0 1 +s_44654 PSG8 0 1 +s_14418 CXCL3 0 1 +s_55464 TAS2R8 0 1 +s_48399 RPUSD2 0 1 +s_913 ACY1 0 1 +s_31805 LRRC71 0 1 +s_5001 BAX 0 1 +s_3317 ARHGAP30 0 1 +s_37868 NR4A3 0 1 +s_30590 LBR 0 1 +s_61178 VCAN 0 1 +s_29591 KLC4 0 1 +s_64356 ZNF639 0 1 +s_59983 TXNRD2 0 1 +s_57475 TMEM212 0 1 +s_5655 BPIFA1 0 1 +s_18849 ETV3 0 1 +s_43527 PPP1R12B 0 1 +s_56080 TEN1 0 2 +s_32594 MAP2 0 1 +s_15939 DHX40 0 1 +s_37655 NPHP1 0 1 +s_39192 OR4D6 0 1 +s_30870 LGALS14 0 2 +s_42366 PLCB2 0 1 +s_52364 SLCO4C1 0 1 +s_38097 NT5DC2 0 1 +s_50596 SHISA6 0 1 +s_5857 BSPRY 0 1 +s_52601 SMG7 0 2 +s_8318 C8A 0 1 +s_16993 DUOX1 0 1 +s_10785 CDH3 0 1 +s_47969 RP11-6F2.7 0 1 +s_10594 CDC20B 0 1 +s_24174 GRM3 0 1 +s_44782 PSMD13 0 1 +s_63594 ZNF276 0 2 +s_13686 CRMP1 0 1 +s_51528 SLC26A9 0 2 +s_27347 IL6R 0 1 +s_11294 CEP41 0 1 +s_41027 PDE8B 0 1 +s_32689 MAP6 0 2 +s_42792 PNCK 0 1 +s_34944 MS4A14 0 1 +s_54480 STON1 0 1 +s_49799 SEMA6D 0 1 +s_42215 PKP3 0 1 +s_27311 IL36G 0 1 +s_11877 CHST13 0 2 +s_43623 PPP1R3F 0 1 +s_38824 OPRM1 0 1 +s_28192 ITSN1 0 1 +s_21104 FIP1L1 0 1 +s_58668 TRAF3IP2 0 1 +s_17459 EEF1D 0 1 +s_1450 AGA 0 1 +s_37258 NLRP3 0 1 +s_30864 LGALS12 0 1 +s_44075 PRKAG2 0 1 +s_19728 FAM193A 0 1 +s_51482 SLC25A5 0 1 +s_61221 VEPH1 0 1 +s_63903 ZNF436 0 1 +s_13290 CPA6 0 1 +s_32131 LY75-CD302 0 1 +s_37502 NOS1 0 1 +s_18145 EML2 0 2 +s_44634 PSG11 0 1 +s_18865 ETV4 0 1 +s_60780 URM1 0 1 +s_37963 NRP2 0 1 +s_49599 SEC14L2 0 1 +s_24936 HDGF 0 1 +s_35013 MSH4 0 1 +s_48860 S100B 0 2 +s_58655 TRAF3 0 1 +s_25157 HESX1 0 1 +s_42544 PLEKHM3 0 1 +s_24430 GTF3C1 0 1 +s_49297 SCML1 0 1 +s_13387 CPO 0 1 +s_55868 TCHH 0 1 +s_6592 C16orf13 0 1 +s_25016 HECTD3 0 1 +s_37084 NIT1 0 1 +s_2729 ANXA11 0 1 +s_600 ACE 0 1 +s_19744 FAM195B 0 1 +s_15563 DEFB119 0 1 +s_46848 RETNLB 0 1 +s_46976 RFXANK 0 1 +s_62881 ZDHHC2 0 1 +s_18600 ERCC4 0 1 +s_56297 TFG 0 1 +s_30446 LAMC1 0 1 +s_2092 ALOX5AP 0 1 +s_63905 ZNF438 0 1 +s_54305 STATH 0 1 +s_64424 ZNF669 0 1 +s_2497 ANKRD18A 0 1 +s_50693 SIGLEC11 0 1 +s_27215 IL22RA1 0 1 +s_21912 G6PC2 0 1 +s_3668 ARNTL2 0 1 +s_64137 ZNF554 0 1 +s_5492 BLOC1S3 0 1 +s_38179 NTSR2 0 1 +s_23343 GNPDA1 0 1 +s_40120 PALM 0 1 +s_38567 OBSL1 0 1 +s_6794 C17orf72 0 1 +s_12522 CMPK2 0 1 +s_27693 IP6K3 0 1 +s_62249 XKR3 0 1 +s_17374 ECT2 0 1 +s_25606 HMGCL 0 1 +s_14107 CTD-2616J11.4 0 1 +s_18531 EPS8L3 0 1 +s_27030 IL12A 0 1 +s_21813 FUZ 0 1 +s_1766 AKAP14 0 1 +s_46068 RAP1GDS1 0 1 +s_56118 TES 0 1 +s_62550 ZBBX 0 1 +s_35964 NACC1 0 1 +s_60449 UGDH 0 1 +s_49668 SEC61A2 0 1 +s_27412 IMPA1 0 1 +s_45961 RAI14 0 1 +s_42305 PLA2R1 0 1 +s_8699 CACNA1G 0 3 +s_44485 PRSS12 0 1 +s_39987 PACRGL 0 1 +s_32700 MAP7 0 1 +s_5056 BBS4 0 1 +s_33958 MINA 0 1 +s_43445 PPM1A 0 1 +s_17811 EIF3E 0 1 +s_12021 CIZ1 0 2 +s_3432 ARHGEF26 0 1 +s_57409 TMEM194A 0 1 +s_31023 LIG4 0 1 +s_49192 SCARB1 0 1 +s_58503 TPD52 0 1 +s_10434 CD44 0 1 +s_18757 ESR2 0 1 +s_9763 CCDC62 0 1 +s_11054 CEACAM1 0 1 +s_42107 PITX3 0 1 +s_10007 CCNA1 0 1 +s_78 AARSD1 0 1 +s_13393 CPOX 0 1 +s_27868 IRF6 0 1 +s_59748 TTYH1 0 1 +s_20080 FAM65C 0 1 +s_28680 KCNJ13 0 1 +s_48414 RQCD1 0 1 +s_48874 S100Z 0 1 +s_12140 CLDN10 0 1 +s_28742 KCNK16 0 1 +s_21781 FUT10 0 1 +s_16607 DOCK3 0 1 +s_63983 ZNF480 0 1 +s_46452 RBM39 0 1 +s_27604 INSM2 0 1 +s_2238 AMMECR1L 0 2 +s_19736 FAM194A 0 1 +s_58968 TRIM52 0 1 +s_48461 RRNAD1 0 1 +s_63217 ZMIZ2 0 1 +s_42123 PJA1 0 1 +s_58259 TNPO3 0 1 +s_8757 CACNG5 0 1 +s_22699 GGCX 0 1 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1 +s_56492 THEM4 0 1 +s_7128 C1orf122 0 1 +s_18445 EPHA8 0 1 +s_56014 TEAD4 0 1 +s_10425 CD40 0 1 +s_64479 ZNF688 0 1 +s_45139 PTPN22 0 1 +s_32474 MAMDC4 0 1 +s_21927 GAB1 0 1 +s_38901 OR10W1 0 1 +s_58633 TRA2B 0 1 +s_19633 FAM178A 0 1 +s_35406 MUC4 0 1 +s_49881 5-Sep 0 1 +s_63487 ZNF223 0 1 +s_19859 FAM213B 0 1 +s_44065 PRKACB 0 1 +s_26987 IKBKG 0 1 +s_18273 ENPP3 0 1 +s_18362 EPB41L1 0 1 +s_786 ACSS2 0 1 +s_44181 PRLH 0 1 +s_52989 SNX8 0 1 +s_45141 PTPN22 0 1 +s_4025 ASS1 0 1 +s_44910 PTCH1 0 1 +s_13662 CRK 0 1 +s_12089 CLCF1 0 1 +s_43122 POLR3G 0 1 +s_5268 BDH1 0 1 +s_54609 STXBP4 0 1 +s_25732 HNRNPCL1 0 1 +s_32962 MATN3 0 1 +s_15113 DCAF6 0 1 +s_40597 PCDHB2 0 1 +s_43158 POMT1 0 1 +s_29627 KLF15 0 1 +s_46321 RBBP5 0 1 +s_636 ACO1 0 1 +s_22316 GATAD2A 0 1 +s_18782 ESYT1 0 1 +s_17442 EDNRB 0 1 +s_49844 SEPP1 0 1 +s_37945 NRL 0 1 +s_1663 AIF1L 0 1 +s_12049 CKLF-CMTM1 0 1 +s_47791 RNF8 0 1 +s_49957 SERPINA3 0 1 +s_36386 NDOR1 0 1 +s_46355 RBFOX3 0 1 +s_38592 OCM2 0 1 +s_54679 SULT1B1 0 1 +s_62114 WNT8A 0 1 +s_64791 ZNF85 0 1 +s_47594 RNF145 0 1 +s_38124 NTM 0 1 +s_12906 COL22A1 0 1 +s_24644 HAAO 0 1 +s_28135 ITM2A 0 1 +s_47786 RNF7 0 1 +s_15988 DIO1 0 1 +s_6200 C11orf49 0 1 +s_37801 NR1H4 0 1 +s_43430 PPIL4 0 1 +s_1661 AIF1 0 1 +s_22033 GAD1 0 1 +s_53153 SOX30 0 1 +s_14364 CWF19L1 0 1 +s_20616 FBXO7 0 1 +s_20861 FGD1 0 1 +s_20325 FAS 0 1 +s_64851 ZNRF3 0 1 +s_13405 CPS1 0 1 +s_10657 CDC42SE2 0 1 +s_27332 IL4I1 0 1 +s_39620 OSBP2 0 1 +s_7970 C4orf37 0 1 +s_2376 ANGPTL6 0 1 +s_9732 CCDC48 0 1 +s_38832 OPTC 0 1 +s_11928 CHUK 0 1 +s_52833 SNRPB2 0 1 diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.countsummary.pdf Binary file test-data/out.countsummary.pdf has changed diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.countsummary.txt --- a/test-data/out.countsummary.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.countsummary.txt Wed Apr 04 11:03:59 2018 -0400 @@ -1,2 +1,2 @@ File Label Reads Mapped Percentage TotalsgRNAs Zerocounts GiniIndex NegSelQC NegSelQCPval NegSelQCPvalPermutation NegSelQCPvalPermutationFDR NegSelQCGene -input.gz sample1 2500 1453 0.5812 2550 1276 0.5267 0 1 1 1 0.0 +input_0.gz test1_fastq_gz 2500 1453 0.5812 2550 1276 0.5267 0 1 1 1 0.0 diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.countsummary_multi.pdf Binary file test-data/out.countsummary_multi.pdf has changed diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.mle.log.txt --- a/test-data/out.mle.log.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.mle.log.txt Wed Apr 04 11:03:59 2018 -0400 @@ -1,749 +1,57 @@ -INFO @ Mon, 12 Feb 2018 21:46:26: Parameters: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/bin/mageck mle -k /tmp/tmpRFR3vr/files/000/dataset_1.dat -d /tmp/tmpRFR3vr/files/000/dataset_2.dat -n output --norm-method median --genes-varmodeling 1000 --permutation-round 10 --adjust-method fdr --threads 1 -INFO @ Mon, 12 Feb 2018 21:46:27: Cannot parse design matrix as a string; try to parse it as a file name ... -INFO @ Mon, 12 Feb 2018 21:46:27: Design matrix: -INFO @ Mon, 12 Feb 2018 21:46:27: [[1. 0. 0.] -INFO @ Mon, 12 Feb 2018 21:46:27: [1. 0. 0.] -INFO @ Mon, 12 Feb 2018 21:46:27: [1. 1. 0.] -INFO @ Mon, 12 Feb 2018 21:46:27: [1. 0. 1.]] -INFO @ Mon, 12 Feb 2018 21:46:27: Beta labels:baseline,HL60,KBM7 -INFO @ Mon, 12 Feb 2018 21:46:27: Included samples:HL60.initial,KBM7.initial,HL60.final,KBM7.final -INFO @ Mon, 12 Feb 2018 21:46:27: Loaded samples:HL60.initial;KBM7.initial;HL60.final;KBM7.final -INFO @ Mon, 12 Feb 2018 21:46:27: Sample index: 0;1;2;3 -INFO @ Mon, 12 Feb 2018 21:46:27: Loaded 100 genes. -DEBUG @ Mon, 12 Feb 2018 21:46:27: Initial (total) size factor: 1.6654412961322171 2.025116092944715 0.720025234995028 0.6592307725342162 -DEBUG @ Mon, 12 Feb 2018 21:46:27: Median factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989 -INFO @ Mon, 12 Feb 2018 21:46:27: Final size factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989 -INFO @ Mon, 12 Feb 2018 21:46:27: size factor: 0.6799984465189518,0.5638048078028025,1.5844800046134337,1.744884273862957 -INFO @ Mon, 12 Feb 2018 21:46:27: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:46:27: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:46:27: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:46:27: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:46:27: All threads completed. -INFO @ Mon, 12 Feb 2018 21:46:27: Modeling the mean and variance ... -INFO @ Mon, 12 Feb 2018 21:46:27: Linear regression: y=-0.902175602829449x+14.539230037913281 -INFO @ Mon, 12 Feb 2018 21:46:27: Run the algorithm for the second time ... -WARNING @ Mon, 12 Feb 2018 21:46:27: A1CF: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:27: A1CF: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:28: A1CF: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:28: A1CF: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:29: A1CF: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:29: A1CF: alpha: 0.09 -INFO @ Mon, 12 Feb 2018 21:46:29: Calculating AAAS (1) ... -WARNING @ Mon, 12 Feb 2018 21:46:29: AAAS: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:29: AAAS: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:30: AAAS: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:30: AAAS: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:31: AAAS: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:31: AAAS: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:31: AAK1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:31: AAK1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:31: AAK1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:31: AAK1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:32: AAK1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:32: AAK1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:32: AATF: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:32: AATF: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:33: AATF: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:33: AATF: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:33: AATF: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:33: AATF: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:33: AATK: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:33: AATK: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:34: AATK: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:34: AATK: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:35: AATK: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:35: AATK: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:35: ABCB8: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:35: ABCB8: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:36: ABCB8: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:36: ABCB8: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:37: ABCB8: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:37: ABCB8: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:37: ABCC1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:37: ABCC1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:38: ABCC1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:38: ABCC1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:38: ABCC1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:38: ABCC1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:38: ABCF1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:38: ABCF1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:39: ABCF1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:39: ABCF1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:40: ABCF1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:40: ABCF1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:40: ABHD14B: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:40: ABHD14B: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:41: ABHD14B: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:41: ABHD14B: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:42: ABHD14B: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:42: ABHD14B: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:42: ABI1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:42: ABI1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:43: ABI1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:43: ABI1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:44: ABI1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:44: ABI1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:44: ABL1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:44: ABL1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:44: ABL1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:44: ABL1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:45: ABL1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:45: ABL1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:45: ABL2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:45: ABL2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:46: ABL2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:46: ABL2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:47: ABL2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:47: ABL2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:47: ABLIM2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:47: ABLIM2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:48: ABLIM2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:48: ABLIM2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:49: ABLIM2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:49: ABLIM2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:49: ABT1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:49: ABT1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:50: ABT1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:50: ABT1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:50: ABTB1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:50: ABTB1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:51: ABTB1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:51: ABTB1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:52: ABTB1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:52: ABTB1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:52: ACAD11: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:52: ACAD11: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:53: ACAD11: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:53: ACAD11: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:54: ACAD11: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:54: ACAD11: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:54: ACAD9: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:54: ACAD9: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:55: ACAD9: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:55: ACAD9: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:55: ACAD9: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:55: ACAD9: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:56: ACAT2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:56: ACAT2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:56: ACAT2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:56: ACAT2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:57: ACAT2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:57: ACAT2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:57: ACBD6: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:57: ACBD6: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:46:58: ACBD6: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:58: ACBD6: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:46:59: ACBD6: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:46:59: ACBD6: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:46:59: ACD: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:46:59: ACD: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:00: ACD: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:00: ACD: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:00: ACD: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:00: ACD: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:00: ACHE: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:00: ACHE: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:01: ACHE: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:01: ACHE: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:02: ACHE: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:02: ACHE: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:02: ACIN1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:02: ACIN1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:03: ACIN1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:03: ACIN1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:04: ACIN1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:04: ACIN1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:04: ACLY: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:04: ACLY: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:05: ACLY: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:05: ACLY: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:05: ACO2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:05: ACO2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:06: ACO2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:06: ACO2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:07: ACO2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:07: ACO2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:07: ACP1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:07: ACP1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:08: ACP1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:08: ACP1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:08: ACP1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:08: ACP1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:08: ACRC: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:08: ACRC: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:09: ACRC: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:09: ACRC: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:10: ACRC: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:10: ACRC: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:10: ACSL6: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:10: ACSL6: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:11: ACSL6: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:11: ACSL6: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:11: ACSL6: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:11: ACSL6: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:11: ACSS2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:11: ACSS2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:12: ACSS2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:12: ACSS2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:13: ACSS2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:13: ACSS2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:13: ACTL6A: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:13: ACTL6A: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:13: ACTL6A: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:13: ACTL6A: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:14: ACTL6A: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:14: ACTL6A: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:14: ACTL6B: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:14: ACTL6B: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:15: ACTL6B: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:15: ACTL6B: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:16: ACTL6B: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:16: ACTL6B: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:16: ACTL7A: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:16: ACTL7A: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:16: ACTL7A: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:16: ACTL7A: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:17: ACTL7A: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:17: ACTL7A: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:17: ACTN1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:17: ACTN1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:18: ACTN1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:18: ACTN1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:19: ACTN1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:19: ACTN1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:19: ACTN4: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:19: ACTN4: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:19: ACTN4: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:19: ACTN4: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:20: ACTN4: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:20: ACTN4: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:20: ACTR1A: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:20: ACTR1A: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:21: ACTR1A: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:21: ACTR1A: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:22: ACTR1A: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:22: ACTR1A: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:22: ACTR3: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:22: ACTR3: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:22: ACTR3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:22: ACTR3: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:23: ACTR3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:23: ACTR3: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:23: ACTR5: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:23: ACTR5: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:24: ACTR5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:24: ACTR5: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:25: ACTR5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:25: ACTR5: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:25: ACTR8: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:25: ACTR8: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:25: ACTR8: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:25: ACTR8: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:26: ACTR8: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:26: ACTR8: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:26: ACTRT3: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:26: ACTRT3: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:27: ACTRT3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:27: ACTRT3: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:28: ACTRT3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:28: ACTRT3: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:28: ACVR1B: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:28: ACVR1B: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:28: ACVR1B: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:28: ACVR1B: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:29: ACVR1B: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:29: ACVR1B: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:29: ACVR1C: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:29: ACVR1C: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:30: ACVR1C: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:30: ACVR1C: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:30: ACVR1C: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:30: ACVR1C: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:30: ACVR1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:30: ACVR1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:31: ACVR1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:31: ACVR1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:32: ACVR1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:32: ACVR1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:32: ACVR2A: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:32: ACVR2A: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:33: ACVR2A: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:33: ACVR2A: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:33: ACVR2A: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:33: ACVR2A: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:33: ACVR2B: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:33: ACVR2B: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:34: ACVR2B: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:34: ACVR2B: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:35: ACVR2B: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:35: ACVR2B: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:35: ACVRL1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:35: ACVRL1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:36: ACVRL1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:36: ACVRL1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:36: ACVRL1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:36: ACVRL1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:36: ADAD1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:36: ADAD1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:37: ADAD1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:37: ADAD1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:38: ADAD1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:38: ADAD1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:38: ADAM10: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:38: ADAM10: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:38: ADAM10: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:38: ADAM10: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:39: ADAM10: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:39: ADAM10: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:39: ADAM12: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:39: ADAM12: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:40: ADAM12: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:40: ADAM12: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:41: ADAM12: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:41: ADAM12: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:41: ADAMTS5: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:41: ADAMTS5: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:41: ADAMTS5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:41: ADAMTS5: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:42: ADAMTS5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:42: ADAMTS5: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:42: ADAP1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:42: ADAP1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:43: ADAP1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:43: ADAP1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:44: ADAP1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:44: ADAP1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:44: ADARB1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:44: ADARB1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:44: ADARB1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:44: ADARB1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:45: ADARB1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:45: ADARB1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:45: ADARB2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:45: ADARB2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:46: ADARB2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:46: ADARB2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:47: ADARB2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:47: ADARB2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:47: ADAR: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:47: ADAR: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:48: ADAR: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:48: ADAR: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:48: ADAR: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:48: ADAR: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:48: ADCK1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:48: ADCK1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:49: ADCK1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:49: ADCK1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:50: ADCK1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:50: ADCK1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:50: ADCK2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:50: ADCK2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:51: ADCK2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:51: ADCK2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:51: ADCK2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:51: ADCK2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:51: ADCK3: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:51: ADCK3: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:52: ADCK3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:52: ADCK3: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:53: ADCK3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:53: ADCK3: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:53: ADCK4: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:53: ADCK4: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:54: ADCK4: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:54: ADCK4: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:54: ADCK4: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:54: ADCK4: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:54: ADCK5: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:54: ADCK5: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:55: ADCK5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:55: ADCK5: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:56: ADCK5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:56: ADCK5: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:56: ADCY1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:56: ADCY1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:57: ADCY1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:57: ADCY1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:57: ADCY1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:57: ADCY1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:57: ADD1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:57: ADD1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:47:58: ADD1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:58: ADD1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:47:59: ADD1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:47:59: ADD1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:47:59: ADD3: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:47:59: ADD3: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:00: ADD3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:00: ADD3: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:00: ADD3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:00: ADD3: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:00: ADH5: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:00: ADH5: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:01: ADH5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:01: ADH5: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:02: ADH5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:02: ADH5: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:02: ADH7: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:02: ADH7: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:03: ADH7: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:03: ADH7: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:04: ADH7: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:04: ADH7: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:04: ADI1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:04: ADI1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:04: ADI1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:04: ADI1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:05: ADI1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:05: ADI1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:06: ADIRF: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:06: ADIRF: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:06: ADIRF: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:06: ADIRF: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:07: ADIRF: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:07: ADIRF: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:07: ADK: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:07: ADK: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:08: ADK: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:08: ADK: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:08: ADK: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:08: ADK: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:09: ADNP2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:09: ADNP2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:09: ADNP2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:09: ADNP2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:10: ADNP2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:10: ADNP2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:10: ADNP: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:10: ADNP: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:11: ADNP: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:11: ADNP: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:12: ADNP: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:12: ADNP: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:12: ADPRHL2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:12: ADPRHL2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:12: ADPRHL2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:12: ADPRHL2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:13: ADPRHL2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:13: ADPRHL2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:13: ADRA1A: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:13: ADRA1A: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:14: ADRA1A: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:14: ADRA1A: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:14: ADRA1A: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:14: ADRA1A: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:14: ADRA1B: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:14: ADRA1B: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:15: ADRA1B: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:15: ADRA1B: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:16: ADRA1B: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:16: ADRA1B: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:16: ADRB1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:16: ADRB1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:17: ADRB1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:17: ADRB1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:18: ADRB1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:18: ADRB1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:18: ADRB2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:18: ADRB2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:19: ADRB2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:19: ADRB2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:20: ADRB2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:20: ADRB2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:20: ADRB3: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:20: ADRB3: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:21: ADRB3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:21: ADRB3: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:21: ADRB3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:21: ADRB3: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:21: ADRBK1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:21: ADRBK1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:22: ADRBK1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:22: ADRBK1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:23: ADRBK1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:23: ADRBK1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:23: ADRBK2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:23: ADRBK2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:24: ADRBK2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:24: ADRBK2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:25: ADRBK2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:25: ADRBK2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:25: ADRM1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:25: ADRM1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:26: ADRM1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:26: ADRM1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:26: ADRM1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:26: ADRM1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:27: AEBP1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:27: AEBP1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:27: AEBP1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:27: AEBP1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:28: AEBP1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:28: AEBP1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:28: AEBP2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:28: AEBP2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:29: AEBP2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:29: AEBP2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:30: AEBP2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:30: AEBP2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:30: AEN: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:30: AEN: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:31: AEN: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:31: AEN: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:31: AEN: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:31: AEN: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:31: AES: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:31: AES: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:32: AES: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:32: AES: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:33: AES: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:33: AES: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:33: AFAP1L2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:33: AFAP1L2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:34: AFAP1L2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:34: AFAP1L2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:34: AFAP1L2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:34: AFAP1L2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:34: AFF1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:34: AFF1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:35: AFF1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:35: AFF1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:36: AFF1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:36: AFF1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:36: AFF2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:36: AFF2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:37: AFF2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:37: AFF2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:37: AFF2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:37: AFF2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:37: AFF3: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:37: AFF3: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:38: AFF3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:38: AFF3: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:39: AFF3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:39: AFF3: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:39: AFF4: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:39: AFF4: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:40: AFF4: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:40: AFF4: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:40: AFF4: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:40: AFF4: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:40: AFMID: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:40: AFMID: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:41: AFMID: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:41: AFMID: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:42: AFMID: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:42: AFMID: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:42: AFTPH: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:42: AFTPH: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:43: AFTPH: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:43: AFTPH: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:43: AFTPH: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:43: AFTPH: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:43: AGAP2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:43: AGAP2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:44: AGAP2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:44: AGAP2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:45: AGAP2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:45: AGAP2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:45: AGAP3: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:45: AGAP3: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:45: AGAP3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:45: AGAP3: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:46: AGAP3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:46: AGAP3: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:46: AGBL5: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:46: AGBL5: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:47: AGBL5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:47: AGBL5: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:48: AGBL5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:48: AGBL5: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:48: AGFG1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:48: AGFG1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:48: AGFG1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:48: AGFG1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:49: AGFG1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:49: AGFG1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:50: AGL: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:50: AGL: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:51: AGL: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:51: AGL: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:51: AGPAT3: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:51: AGPAT3: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:52: AGPAT3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:52: AGPAT3: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:52: AGPAT3: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:52: AGPAT3: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:52: AGPAT5: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:52: AGPAT5: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:53: AGPAT5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:53: AGPAT5: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:54: AGPAT5: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:54: AGPAT5: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:54: AGTPBP1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:54: AGTPBP1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:55: AGTPBP1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:55: AGTPBP1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:55: AGTPBP1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:55: AGTPBP1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:55: AHCTF1: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:55: AHCTF1: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:56: AHCTF1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:56: AHCTF1: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:57: AHCTF1: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:57: AHCTF1: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:57: AHCY: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:57: AHCY: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:58: AHCY: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:58: AHCY: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:48:58: AHCY: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:58: AHCY: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:48:58: AHNAK2: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:48:58: AHNAK2: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:48:59: AHNAK2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:48:59: AHNAK2: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:49:00: AHNAK2: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:49:00: AHNAK2: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:49:01: AHNAK: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:49:01: AHNAK: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:49:01: AHNAK: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:49:01: AHNAK: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:49:02: AHNAK: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:49:02: AHNAK: alpha: 0.09 -WARNING @ Mon, 12 Feb 2018 21:49:02: AHRR: beta value does not converge. Try to increase the value of alpha .. -WARNING @ Mon, 12 Feb 2018 21:49:02: AHRR: alpha: 0.01 -WARNING @ Mon, 12 Feb 2018 21:49:03: AHRR: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:49:03: AHRR: alpha: 0.03 -WARNING @ Mon, 12 Feb 2018 21:49:04: AHRR: reaches the maximum number of iterations. -WARNING @ Mon, 12 Feb 2018 21:49:04: AHRR: alpha: 0.09 -INFO @ Mon, 12 Feb 2018 21:49:04: Permuting groups of gene with 9 sgRNAs per gene. Group progress: 1/2 -INFO @ Mon, 12 Feb 2018 21:49:04: Start permuting 10 rounds ... -INFO @ Mon, 12 Feb 2018 21:49:04: Collecting 999 sgRNAs from 100 genes. -INFO @ Mon, 12 Feb 2018 21:49:04: Permuting round 0 ... -INFO @ Mon, 12 Feb 2018 21:49:04: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:04: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:04: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:04: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:04: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:04: Permuting round 1 ... -INFO @ Mon, 12 Feb 2018 21:49:05: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:05: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:05: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:05: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:05: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:05: Permuting round 2 ... -INFO @ Mon, 12 Feb 2018 21:49:05: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:05: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:05: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:06: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:06: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:06: Permuting round 3 ... -INFO @ Mon, 12 Feb 2018 21:49:06: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:06: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:06: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:07: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:07: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:07: Permuting round 4 ... -INFO @ Mon, 12 Feb 2018 21:49:07: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:07: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:07: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:08: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:08: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:08: Permuting round 5 ... -INFO @ Mon, 12 Feb 2018 21:49:08: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:08: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:08: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:09: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:09: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:09: Permuting round 6 ... -INFO @ Mon, 12 Feb 2018 21:49:09: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:09: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:09: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:09: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:09: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:10: Permuting round 7 ... -INFO @ Mon, 12 Feb 2018 21:49:10: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:10: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:10: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:10: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:10: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:10: Permuting round 8 ... -INFO @ Mon, 12 Feb 2018 21:49:10: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:10: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:10: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:11: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:11: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:11: Permuting round 9 ... -INFO @ Mon, 12 Feb 2018 21:49:11: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:11: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:11: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:12: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:12: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:12: Assigning p values... -INFO @ Mon, 12 Feb 2018 21:49:12: Permuting groups of gene with 10 sgRNAs per gene. Group progress: 2/2 -INFO @ Mon, 12 Feb 2018 21:49:12: Start permuting 10 rounds ... -INFO @ Mon, 12 Feb 2018 21:49:12: Collecting 999 sgRNAs from 100 genes. -INFO @ Mon, 12 Feb 2018 21:49:12: Permuting round 0 ... -INFO @ Mon, 12 Feb 2018 21:49:12: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:12: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:12: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:13: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:13: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:13: Permuting round 1 ... -INFO @ Mon, 12 Feb 2018 21:49:13: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:13: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:13: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:14: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:14: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:14: Permuting round 2 ... -INFO @ Mon, 12 Feb 2018 21:49:14: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:14: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:14: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:15: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:15: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:15: Permuting round 3 ... -INFO @ Mon, 12 Feb 2018 21:49:15: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:15: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:15: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:16: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:16: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:16: Permuting round 4 ... -INFO @ Mon, 12 Feb 2018 21:49:16: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:16: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:16: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:16: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:16: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:17: Permuting round 5 ... -INFO @ Mon, 12 Feb 2018 21:49:17: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:17: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:17: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:17: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:17: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:18: Permuting round 6 ... -INFO @ Mon, 12 Feb 2018 21:49:18: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:18: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:18: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:19: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:19: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:19: Permuting round 7 ... -INFO @ Mon, 12 Feb 2018 21:49:19: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:19: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:19: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:20: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:20: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:20: Permuting round 8 ... -INFO @ Mon, 12 Feb 2018 21:49:20: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:20: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:20: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:21: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:21: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:21: Permuting round 9 ... -INFO @ Mon, 12 Feb 2018 21:49:21: Thread 0 started. -INFO @ Mon, 12 Feb 2018 21:49:21: Thread 0: total 100 instances. -INFO @ Mon, 12 Feb 2018 21:49:21: Thread 0: Calculating AAAS (1) ... -INFO @ Mon, 12 Feb 2018 21:49:21: Thread 0 completed. -INFO @ Mon, 12 Feb 2018 21:49:21: All threads completed. -INFO @ Mon, 12 Feb 2018 21:49:22: Assigning p values... -INFO @ Mon, 12 Feb 2018 21:49:22: Writing gene results to output.gene_summary.txt -INFO @ Mon, 12 Feb 2018 21:49:22: Writing sgRNA results to output.sgrna_summary.txt +INFO @ Sun, 25 Mar 2018 22:27:41: Parameters: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/bin/mageck mle -k /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpELNsjE/files/000/dataset_28.dat -d /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpELNsjE/files/000/dataset_29.dat -n output --norm-method median --threads 1 +INFO @ Sun, 25 Mar 2018 22:27:42: Cannot parse design matrix as a string; try to parse it as a file name ... +INFO @ Sun, 25 Mar 2018 22:27:42: Design matrix: +INFO @ Sun, 25 Mar 2018 22:27:42: [[1. 0. 0.] +INFO @ Sun, 25 Mar 2018 22:27:42: [1. 0. 0.] +INFO @ Sun, 25 Mar 2018 22:27:42: [1. 1. 0.] +INFO @ Sun, 25 Mar 2018 22:27:42: [1. 0. 1.]] +INFO @ Sun, 25 Mar 2018 22:27:42: Beta labels:baseline,HL60,KBM7 +INFO @ Sun, 25 Mar 2018 22:27:42: Included samples:HL60.initial,KBM7.initial,HL60.final,KBM7.final +INFO @ Sun, 25 Mar 2018 22:27:42: Loaded samples:HL60.initial;KBM7.initial;HL60.final;KBM7.final +INFO @ Sun, 25 Mar 2018 22:27:42: Sample index: 0;1;2;3 +INFO @ Sun, 25 Mar 2018 22:27:42: Loaded 100 genes. +DEBUG @ Sun, 25 Mar 2018 22:27:42: Initial (total) size factor: 1.6654412961322171 2.025116092944715 0.720025234995028 0.6592307725342162 +DEBUG @ Sun, 25 Mar 2018 22:27:42: Median factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989 +INFO @ Sun, 25 Mar 2018 22:27:42: Final size factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989 +INFO @ Sun, 25 Mar 2018 22:27:42: size factor: 0.6799984465189518,0.5638048078028025,1.5844800046134337,1.744884273862957 +INFO @ Sun, 25 Mar 2018 22:27:42: Thread 0 started. +INFO @ Sun, 25 Mar 2018 22:27:42: Thread 0: total 1 instances. +INFO @ Sun, 25 Mar 2018 22:27:42: Thread 0 completed. +INFO @ Sun, 25 Mar 2018 22:27:42: All threads completed. +INFO @ Sun, 25 Mar 2018 22:27:42: Modeling the mean and variance ... +INFO @ Sun, 25 Mar 2018 22:27:42: Run the algorithm for the second time ... +INFO @ Sun, 25 Mar 2018 22:27:42: Calculating AAAS (1) ... +INFO @ Sun, 25 Mar 2018 22:27:43: Permuting groups of gene with 9 sgRNAs per gene. Group progress: 1/2 +INFO @ Sun, 25 Mar 2018 22:27:43: Start permuting 2 rounds ... +INFO @ Sun, 25 Mar 2018 22:27:43: Collecting 999 sgRNAs from 100 genes. +INFO @ Sun, 25 Mar 2018 22:27:43: Permuting round 0 ... +INFO @ Sun, 25 Mar 2018 22:27:43: Thread 0 started. +INFO @ Sun, 25 Mar 2018 22:27:43: Thread 0: total 100 instances. +INFO @ Sun, 25 Mar 2018 22:27:43: Thread 0: Calculating AAAS (1) ... +INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0 completed. +INFO @ Sun, 25 Mar 2018 22:27:45: All threads completed. +INFO @ Sun, 25 Mar 2018 22:27:45: Permuting round 1 ... +INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0 started. +INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0: total 100 instances. +INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0: Calculating AAAS (1) ... +INFO @ Sun, 25 Mar 2018 22:27:46: Thread 0 completed. +INFO @ Sun, 25 Mar 2018 22:27:46: All threads completed. +INFO @ Sun, 25 Mar 2018 22:27:46: Assigning p values... +INFO @ Sun, 25 Mar 2018 22:27:46: Permuting groups of gene with 10 sgRNAs per gene. Group progress: 2/2 +INFO @ Sun, 25 Mar 2018 22:27:46: Start permuting 2 rounds ... +INFO @ Sun, 25 Mar 2018 22:27:46: Collecting 999 sgRNAs from 100 genes. +INFO @ Sun, 25 Mar 2018 22:27:46: Permuting round 0 ... +INFO @ Sun, 25 Mar 2018 22:27:47: Thread 0 started. +INFO @ Sun, 25 Mar 2018 22:27:47: Thread 0: total 100 instances. +INFO @ Sun, 25 Mar 2018 22:27:47: Thread 0: Calculating AAAS (1) ... +INFO @ Sun, 25 Mar 2018 22:27:48: Thread 0 completed. +INFO @ Sun, 25 Mar 2018 22:27:48: All threads completed. +INFO @ Sun, 25 Mar 2018 22:27:49: Permuting round 1 ... +INFO @ Sun, 25 Mar 2018 22:27:49: Thread 0 started. +INFO @ Sun, 25 Mar 2018 22:27:49: Thread 0: total 100 instances. +INFO @ Sun, 25 Mar 2018 22:27:49: Thread 0: Calculating AAAS (1) ... +INFO @ Sun, 25 Mar 2018 22:27:50: Thread 0 completed. +INFO @ Sun, 25 Mar 2018 22:27:50: All threads completed. +INFO @ Sun, 25 Mar 2018 22:27:50: Assigning p values... +INFO @ Sun, 25 Mar 2018 22:27:50: Writing gene results to output.gene_summary.txt +INFO @ Sun, 25 Mar 2018 22:27:50: Writing sgRNA results to output.sgrna_summary.txt diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.normcounts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.normcounts.txt Wed Apr 04 11:03:59 2018 -0400 @@ -0,0 +1,2551 @@ +sgRNA Gene test1_fastq_gz +s_47512 RNF111 2.0 +s_24835 HCFC1R1 2.0 +s_14784 CYP4B1 8.0 +s_51146 SLC18A1 2.0 +s_58960 TRIM5 2.0 +s_48256 RPRD2 2.0 +s_30297 KRTAP5-5 2.0 +s_14555 CYB5B 2.0 +s_39959 PAAF1 2.0 +s_45293 PUF60 2.0 +s_49358 SCN8A 2.0 +s_64995 ZYG11A 2.0 +s_4029 ASTE1 2.0 +s_45554 R3HDML 2.0 +s_34264 MMRN1 2.0 +s_37459 NOL6 2.0 +s_23990 GPX7 2.0 +s_20268 FANCC 2.0 +s_14157 CTLA4 2.0 +s_36773 NEURL4 36.0 +s_18804 ETFB 2.0 +s_782 ACSS1 2.0 +s_18272 ENPP2 2.0 +s_46620 RCN1 2.0 +s_55436 TAS2R3 2.0 +s_57947 TMPRSS2 2.0 +s_6438 C14orf159 2.0 +s_33846 MGST2 2.0 +s_16328 DNAH6 2.0 +s_17875 EIF4G1 2.0 +s_2305 ANAPC11 2.0 +s_2500 ANKRD2 2.0 +s_82 AARSD1 2.0 +s_55329 TAL1 2.0 +s_57926 TMPRSS11E 16.0 +s_38414 NUP98 8.0 +s_50044 SERPINF1 2.0 +s_9257 CASR 2.0 +s_63396 ZNF182 2.0 +s_56478 THBS3 2.0 +s_17191 DYRK1A 2.0 +s_11988 CIR1 2.0 +s_43313 PPARD 2.0 +s_44681 PSMA4 2.0 +s_10387 CD320 2.0 +s_64869 ZPBP 2.0 +s_54385 STK17B 2.0 +s_25423 HIST1H4D 2.0 +s_54172 ST8SIA4 18.0 +s_1161 ADCY10 2.0 +s_29184 KIAA0913 2.0 +s_42977 POLD3 2.0 +s_49449 SCUBE1 2.0 +s_24181 GRM4 2.0 +s_52507 SMARCA5 2.0 +s_28674 KCNJ10 2.0 +s_61074 VAMP2 8.0 +s_3954 ASIC2 2.0 +s_2385 ANK1 2.0 +s_18397 EPDR1 2.0 +s_18377 EPB41L4B 2.0 +s_34580 MRAP2 2.0 +s_48676 RUFY3 20.0 +s_691 ACP1 2.0 +s_30460 LAMP2 2.0 +s_42637 PLRG1 2.0 +s_12695 CNOT6 2.0 +s_33316 MECOM 4.0 +s_35081 MSRB2 2.0 +s_58512 TPD52L2 2.0 +s_19912 FAM22F 2.0 +s_45517 QSOX2 2.0 +s_56705 TINAG 2.0 +s_10946 CDKL5 2.0 +s_57473 TMEM211 4.0 +s_57657 TMEM44 2.0 +s_43200 POT1 2.0 +s_19436 FAM135A 2.0 +s_184 ABCB9 2.0 +s_30171 KRT84 2.0 +s_44758 PSMC3IP 2.0 +s_48313 RPS3 2.0 +s_58142 TNFSF12 12.0 +s_59718 TTLL6 14.0 +s_9725 CCDC43 2.0 +s_5135 BCKDHA 2.0 +s_36539 NDUFC2 2.0 +s_27251 IL27RA 2.0 +s_48939 SAMD10 2.0 +s_27343 IL5RA 2.0 +s_28386 KANK2 2.0 +s_27610 INSRR 2.0 +s_2769 AOC3 4.0 +s_58632 TRA2B 24.0 +s_6674 C16orf86 2.0 +s_22902 GJD4 2.0 +s_48278 RPS15A 2.0 +s_61998 WIPF2 2.0 +s_4937 BAIAP3 4.0 +s_54471 STOML1 4.0 +s_19157 FABP12 2.0 +s_5434 BIN1 4.0 +s_42042 PIP5K1A 2.0 +s_7794 C3orf18 2.0 +s_54846 SVIL 2.0 +s_62273 XPA 2.0 +s_45859 RACGAP1 2.0 +s_53626 SPOCK3 2.0 +s_43295 PPAP2C 14.0 +s_11788 CHRDL1 4.0 +s_50636 SHQ1 2.0 +s_16705 DPF1 2.0 +s_39741 OTOF 2.0 +s_27505 INHBE 2.0 +s_707 ACPL2 2.0 +s_15418 DDX3Y 12.0 +s_56018 TEAD4 2.0 +s_44367 PRR12 2.0 +s_25875 HOXB5 2.0 +s_49360 SCN9A 2.0 +s_16244 DMPK 2.0 +s_3909 ASCC2 2.0 +s_55088 SYT6 2.0 +s_54311 STAU1 2.0 +s_53890 SRP72 2.0 +s_11035 CDX1 2.0 +s_18178 EMR3 4.0 +s_16084 DLD 2.0 +s_47207 RHOBTB1 2.0 +s_40267 PARK2 12.0 +s_43104 POLR3B 2.0 +s_2200 AMDHD2 2.0 +s_12738 CNRIP1 2.0 +s_17842 EIF4A3 2.0 +s_57950 TMPRSS3 2.0 +s_62146 WRN 2.0 +s_11055 CEACAM1 2.0 +s_54580 STX2 2.0 +s_29277 KIAA1407 2.0 +s_33428 MEF2A 2.0 +s_59797 TUBB 2.0 +s_18113 EME1 2.0 +s_29839 KLHL8 2.0 +s_18058 ELP2 2.0 +s_49497 SDCBP2 6.0 +s_16874 DRP2 2.0 +s_13572 CREBL2 2.0 +s_20540 FBXO30 2.0 +s_64380 ZNF646 2.0 +s_50366 SH2B1 2.0 +s_2548 ANKRD33B 2.0 +s_41183 PDXP 2.0 +s_16315 DNAH12 2.0 +s_19996 FAM49B 2.0 +s_30751 LDLRAD3 2.0 +s_36960 NGEF 2.0 +s_39015 OR2A2 2.0 +s_26302 HSPB2 2.0 +s_64297 ZNF611 10.0 +s_730 ACSBG1 2.0 +s_50271 SFXN4 2.0 +s_8592 CA6 4.0 +s_13683 CRMP1 2.0 +s_51103 SLC16A7 2.0 +s_63785 ZNF384 2.0 +s_16339 DNAH9 2.0 +s_55936 TCTEX1D1 2.0 +s_14497 CXorf40A 2.0 +s_1123 ADAT1 2.0 +s_41304 PERP 2.0 +s_18719 ESAM 2.0 +s_35118 MSX2 2.0 +s_30128 KRT6A 2.0 +s_402 ABTB1 2.0 +s_32578 MAP1LC3A 2.0 +s_45063 PTMA 2.0 +s_43551 PPP1R14D 2.0 +s_2538 ANKRD32 2.0 +s_40384 PAX1 2.0 +s_29076 KIAA0101 2.0 +s_40482 PCDH10 2.0 +s_2348 ANGPT2 2.0 +s_59756 TTYH3 2.0 +s_34330 MOB4 2.0 +s_49331 SCN2B 2.0 +s_54905 SYDE1 2.0 +s_39101 OR2T1 2.0 +s_36623 NEDD4L 2.0 +s_40500 PCDH15 4.0 +s_10660 CDC42SE2 2.0 +s_30867 LGALS13 2.0 +s_24322 GSTK1 4.0 +s_59167 TRPC1 2.0 +s_57440 TMEM201 2.0 +s_50539 SHC1 2.0 +s_37087 NIT1 2.0 +s_56345 TGFB2 2.0 +s_55388 TARM1 2.0 +s_1224 ADD2 2.0 +s_5256 BCOR 4.0 +s_51731 SLC35B3 2.0 +s_12987 COL6A6 2.0 +s_56745 TJP3 2.0 +s_19340 FAM120AOS 2.0 +s_53904 SRPR 2.0 +s_1588 AGXT 2.0 +s_46157 RASA3 2.0 +s_19166 FABP3 14.0 +s_22330 GATM 2.0 +s_10731 CDH13 2.0 +s_2329 ANAPC5 2.0 +s_46045 RANGAP1 2.0 +s_54814 SUV39H2 2.0 +s_56169 TEX14 2.0 +s_3433 ARHGEF26 2.0 +s_48032 RP4-811H24.6 2.0 +s_51930 SLC41A3 2.0 +s_63893 ZNF433 2.0 +s_46996 RGCC 2.0 +s_13863 CSF3R 2.0 +s_26337 HSPH1 2.0 +s_12983 COL6A3 2.0 +s_1376 ADSS 2.0 +s_45449 PYHIN1 2.0 +s_49629 SEC22C 2.0 +s_20204 FAM86A 2.0 +s_24920 HDAC9 2.0 +s_14961 DAPK1 2.0 +s_23900 GPR98 4.0 +s_14485 CXorf27 2.0 +s_61808 WDR66 2.0 +s_55855 TCF7 2.0 +s_44652 PSG8 2.0 +s_46608 RCCD1 2.0 +s_61175 VCAM1 2.0 +s_27453 INCA1 2.0 +s_28987 KDM4C 2.0 +s_20613 FBXO7 2.0 +s_7715 C2orf70 6.0 +s_3902 ASB9 2.0 +s_64098 ZNF534 2.0 +s_31108 LIN7B 2.0 +s_3383 ARHGEF1 2.0 +s_7626 C2orf43 2.0 +s_52247 SLC8A1 2.0 +s_54498 STOX1 2.0 +s_12160 CLDN17 2.0 +s_16224 DMD 2.0 +s_41715 PHLDB2 2.0 +s_12197 CLDN7 2.0 +s_51239 SLC22A16 2.0 +s_41286 PEPD 2.0 +s_2367 ANGPTL4 2.0 +s_59289 TSC22D4 2.0 +s_22437 GCFC2 2.0 +s_24343 GSTO2 2.0 +s_32783 MAPKAPK5 2.0 +s_37032 NINJ1 2.0 +s_49065 SASH3 2.0 +s_60466 UGT1A1 2.0 +s_26043 HPSE2 4.0 +s_21199 FLNA 2.0 +s_41054 PDGFRA 2.0 +s_1820 AKNA 2.0 +s_19548 FAM166A 2.0 +s_43967 PRDX5 2.0 +s_51905 SLC39A8 2.0 +s_22723 GGT5 10.0 +s_13242 COX6C 2.0 +s_27668 IP6K1 2.0 +s_64491 ZNF692 2.0 +s_61982 WHSC1L1 4.0 +s_48495 RSAD1 2.0 +s_34351 MOCS3 2.0 +s_12069 CLCA1 6.0 +s_22023 GABRR1 2.0 +s_12812 COASY 4.0 +s_40068 PAIP1 2.0 +s_11513 CGREF1 4.0 +s_32119 LY6K 2.0 +s_60743 UQCR11 2.0 +s_56354 TGFBR1 2.0 +s_3062 APOL2 2.0 +s_20525 FBXO25 2.0 +s_55591 TBC1D7 2.0 +s_14987 DARS2 2.0 +s_63195 ZMAT2 2.0 +s_41936 PIK3C2G 2.0 +s_56092 TEP1 2.0 +s_61284 VIT 2.0 +s_10035 CCND2 2.0 +s_43744 PPP6R3 4.0 +s_48110 RPL10L 2.0 +s_39381 OR5H15 2.0 +s_6827 C17orf90 4.0 +s_8795 CADPS 2.0 +s_55301 TAF9 2.0 +s_25756 HNRNPM 2.0 +s_61177 VCAN 2.0 +s_22932 GLB1 2.0 +s_55751 TCEA2 2.0 +s_39419 OR5T3 2.0 +s_33669 MEX3A 2.0 +s_42714 PLXNC1 2.0 +s_23239 GNAT1 2.0 +s_4546 ATPAF1 2.0 +s_64432 ZNF671 2.0 +s_31346 LOXHD1 2.0 +s_46353 RBFOX2 2.0 +s_8848 CALHM2 2.0 +s_27039 IL12RB1 2.0 +s_62824 ZCCHC9 2.0 +s_7498 C20orf96 2.0 +s_43406 PPIE 2.0 +s_54925 SYN1 2.0 +s_27284 IL31RA 2.0 +s_63774 ZNF37A 2.0 +s_43643 PPP1R8 2.0 +s_63149 ZIC2 2.0 +s_26251 HSP90AB1 2.0 +s_46773 RELL2 2.0 +s_64868 ZP4 2.0 +s_626 ACLY 2.0 +s_40694 PCED1A 2.0 +s_15888 DHTKD1 2.0 +s_53641 SPP1 2.0 +s_21822 FXR1 2.0 +s_53660 SPR 2.0 +s_29906 KLKB1 2.0 +s_1901 ALAS2 2.0 +s_45130 PTPN2 2.0 +s_43535 PPP1R13B 4.0 +s_15855 DHRS12 2.0 +s_13602 CRH 2.0 +s_51848 SLC39A1 2.0 +s_61205 VDR 2.0 +s_18989 EXOC7 2.0 +s_22294 GATA1 4.0 +s_34584 MRAS 2.0 +s_33140 MCFD2 2.0 +s_34546 MPST 2.0 +s_27208 IL21R 2.0 +s_14576 CYB5R4 2.0 +s_43745 PPP6R3 2.0 +s_41675 PHF8 2.0 +s_41243 PEBP4 4.0 +s_42685 PLXNA1 2.0 +s_41585 PHB2 2.0 +s_47989 RP1L1 2.0 +s_42300 PLA2G6 2.0 +s_53387 SPATA6L 2.0 +s_15423 DDX4 2.0 +s_64039 ZNF506 10.0 +s_22276 GAS6 2.0 +s_15373 DDX19B 2.0 +s_4322 ATP2B2 2.0 +s_25787 HOMER1 2.0 +s_10739 CDH16 2.0 +s_51702 SLC34A3 2.0 +s_20623 FBXO9 4.0 +s_13244 COX6C 2.0 +s_35367 MTX2 2.0 +s_5681 BPIFB6 2.0 +s_57337 TMEM176A 2.0 +s_43464 PPM1F 2.0 +s_20530 FBXO28 2.0 +s_55958 TDGF1 2.0 +s_4516 ATP7B 2.0 +s_19128 F8 2.0 +s_40084 PAK1IP1 2.0 +s_29430 KIF20B 2.0 +s_14773 CYP46A1 2.0 +s_19102 F2R 2.0 +s_29306 KIAA1524 4.0 +s_11438 CETN3 2.0 +s_49647 SEC24D 2.0 +s_35891 NAA11 2.0 +s_10770 CDH23 4.0 +s_44838 PSMG2 2.0 +s_22687 GGCT 2.0 +s_14266 CTSW 2.0 +s_38451 NXF3 2.0 +s_60012 TYRP1 2.0 +s_13190 COTL1 2.0 +s_4721 AZI2 2.0 +s_28800 KCNMB3 2.0 +s_23136 GM2A 2.0 +s_31806 LRRC71 2.0 +s_11862 CHRNG 4.0 +s_52893 SNX12 2.0 +s_31960 LSM5 2.0 +s_3273 ARHGAP22 2.0 +s_22140 GALNT2 2.0 +s_36663 NEK1 2.0 +s_45974 RALB 2.0 +s_48582 RTCA 2.0 +s_27173 IL1RL1 2.0 +s_49800 SEMA6D 2.0 +s_18249 ENOPH1 2.0 +s_31609 LRRC10B 2.0 +s_6450 C14orf176 2.0 +s_42314 PLAC1L 2.0 +s_7822 C3orf27 2.0 +s_43695 PPP2R5C 2.0 +s_8939 CAMKV 2.0 +s_58681 TRAF7 2.0 +s_12850 COG6 2.0 +s_20936 FGF3 2.0 +s_10862 CDK17 2.0 +s_60046 UAP1 2.0 +s_42295 PLA2G5 2.0 +s_52045 SLC4A9 2.0 +s_18532 EPS8L3 2.0 +s_15737 DFNB31 2.0 +s_12691 CNOT4 2.0 +s_27651 INTS7 2.0 +s_52454 SLX4 2.0 +s_5507 BMF 2.0 +s_57583 TMEM25 2.0 +s_36267 NCK2 2.0 +s_15361 DDX17 2.0 +s_24303 GSS 2.0 +s_11095 CEBPB 4.0 +s_59318 TSG101 2.0 +s_35897 NAA16 2.0 +s_11714 CHMP3 2.0 +s_7217 C1orf186 2.0 +s_14282 CTU1 2.0 +s_53137 SOX15 2.0 +s_30977 LHX3 2.0 +s_825 ACTL6A 2.0 +s_33214 MCOLN3 2.0 +s_57706 TMEM55B 2.0 +s_41619 PHF12 2.0 +s_13595 CREM 2.0 +s_30523 LARP4 2.0 +s_6229 C11orf68 2.0 +s_17880 EIF4G2 2.0 +s_36676 NEK3 2.0 +s_23667 GPR123 2.0 +s_1296 ADORA1 2.0 +s_18235 ENHO 2.0 +s_20589 FBXO45 2.0 +s_31341 LOX 2.0 +s_20983 FGFR2 2.0 +s_44192 PRLR 2.0 +s_62014 WIPI2 2.0 +s_2585 ANKRD45 2.0 +s_14161 CTLA4 2.0 +s_63079 ZFYVE1 2.0 +s_7088 C1orf106 2.0 +s_10461 CD55 2.0 +s_24803 HBM 2.0 +s_52929 SNX21 2.0 +s_40041 PAFAH2 2.0 +s_17056 DUSP15 2.0 +s_61656 WDR12 2.0 +s_28830 KCNQ3 4.0 +s_44745 PSMB9 2.0 +s_16151 DLGAP5 2.0 +s_17799 EIF2S3 2.0 +s_49444 SCTR 2.0 +s_37203 NLGN3 2.0 +s_63798 ZNF385D 2.0 +s_42282 PLA2G4D 2.0 +s_27383 ILF3 2.0 +s_40974 PDE4DIP 2.0 +s_55037 SYT1 2.0 +s_52560 SMC6 2.0 +s_56910 TM9SF2 2.0 +s_64839 ZNHIT6 4.0 +s_20818 FES 2.0 +s_16789 DPY19L3 2.0 +s_46072 RAP2A 2.0 +s_24369 GTDC1 2.0 +s_5332 BEST3 2.0 +s_15793 DGKG 4.0 +s_13197 COX11 2.0 +s_1613 AHCYL1 2.0 +s_62445 YLPM1 2.0 +s_5441 BIN3 2.0 +s_20572 FBXO41 2.0 +s_26507 IBSP 2.0 +s_17166 DYNC2H1 2.0 +s_37694 NPNT 2.0 +s_62561 ZBP1 2.0 +s_28074 ITGB3BP 2.0 +s_13046 COMMD4 2.0 +s_4936 BAIAP3 2.0 +s_16345 DNAI1 4.0 +s_60141 UBE2D4 2.0 +s_34569 MPZL3 2.0 +s_35839 MYRIP 2.0 +s_42840 PNN 2.0 +s_64147 ZNF558 2.0 +s_21759 FUCA2 2.0 +s_62347 XYLB 2.0 +s_41049 PDGFD 2.0 +s_19760 FAM198B 2.0 +s_4944 BAMBI 2.0 +s_59471 TSSC1 2.0 +s_60224 UBE2T 2.0 +s_62753 ZC3H6 2.0 +s_29129 KIAA0355 2.0 +s_43266 PPA2 2.0 +s_48165 RPL31 2.0 +s_25918 HOXC8 2.0 +s_61309 VMO1 2.0 +s_29649 KLF5 2.0 +s_3093 APP 2.0 +s_59201 TRPM2 4.0 +s_31154 LIPH 2.0 +s_43571 PPP1R17 2.0 +s_58112 TNFRSF25 2.0 +s_22767 GHRL 2.0 +s_59817 TUBB6 2.0 +s_63192 ZMAT1 2.0 +s_7306 C1orf49 2.0 +s_37585 NOX5 2.0 +s_57817 TMEM87B 2.0 +s_3667 ARNTL2 2.0 +s_14264 CTSS 2.0 +s_61283 VIT 2.0 +s_35482 MXD3 4.0 +s_54197 STAC2 2.0 +s_54806 SUSD5 2.0 +s_22238 GAPT 2.0 +s_62113 WNT8A 2.0 +s_54543 STRN4 2.0 +s_33235 MDC1 2.0 +s_63489 ZNF224 2.0 +s_37914 NRG1 2.0 +s_36452 NDUFA3 2.0 +s_12262 CLEC3B 2.0 +s_25 AAAS 2.0 +s_50339 SGPP2 2.0 +s_30706 LDB1 2.0 +s_49357 SCN8A 2.0 +s_33618 METTL21D 2.0 +s_4402 ATP5O 2.0 +s_55017 SYNRG 2.0 +s_51299 SLC23A3 2.0 +s_34572 MR1 4.0 +s_49259 SCGB3A1 2.0 +s_17794 EIF2S1 2.0 +s_47977 RP11-744I24.1 2.0 +s_32701 MAP7 2.0 +s_32432 MAGI3 2.0 +s_36564 NDUFS6 2.0 +s_11527 CHAC1 2.0 +s_56181 TEX22 2.0 +s_714 ACPT 2.0 +s_51144 SLC18A1 2.0 +s_57122 TMEM117 2.0 +s_28872 KCTD1 2.0 +s_63600 ZNF28 2.0 +s_57369 TMEM182 2.0 +s_60388 UCK1 2.0 +s_47188 RHEB 2.0 +s_15237 DCTD 2.0 +s_42694 PLXNA4 2.0 +s_19680 FAM187B 2.0 +s_35378 MUC1 2.0 +s_38682 OGG1 2.0 +s_1085 ADAMTS9 2.0 +s_40910 PDE1A 2.0 +s_27956 ISOC2 2.0 +s_27821 IRAK1 2.0 +s_16210 DMBT1 2.0 +s_63398 ZNF184 2.0 +s_18679 ERMP1 2.0 +s_9161 CASC1 4.0 +s_45196 PTPRF 2.0 +s_23002 GLIS2 2.0 +s_17310 EBP 2.0 +s_54797 SUSD3 2.0 +s_1528 AGPAT4 2.0 +s_7045 C1QTNF6 2.0 +s_22952 GLCE 2.0 +s_7105 C1orf111 2.0 +s_36537 NDUFC1 2.0 +s_15359 DDX11 2.0 +s_32881 MARK3 2.0 +s_27486 INHA 2.0 +s_2399 ANK2 2.0 +s_60825 USP10 2.0 +s_20838 FEZ2 2.0 +s_43974 PREB 2.0 +s_16482 DNAJC5G 2.0 +s_26334 HSPG2 2.0 +s_46175 RASD1 2.0 +s_26764 IFT20 2.0 +s_14739 CYP2J2 2.0 +s_11386 CERS2 2.0 +s_5964 BTN1A1 2.0 +s_16810 DPYSL3 2.0 +s_16136 DLGAP2 2.0 +s_13401 CPPED1 2.0 +s_22359 GBGT1 2.0 +s_49575 SDSL 2.0 +s_62067 WNT16 2.0 +s_61863 WDR83OS 2.0 +s_44742 PSMB8 4.0 +s_31855 LRRFIP2 2.0 +s_528 ACADM 2.0 +s_13073 COPA 2.0 +s_32741 MAPK3 2.0 +s_38779 OPA3 2.0 +s_34827 MRPS17 2.0 +s_16969 DTX1 2.0 +s_56448 THAP4 2.0 +s_906 ACVR2A 2.0 +s_45078 PTP4A2 2.0 +s_23628 GPR101 2.0 +s_58510 TPD52L1 2.0 +s_561 ACAT2 2.0 +s_52492 SMAP2 2.0 +s_24039 GRB2 2.0 +s_46264 RASSF4 2.0 +s_39609 ORMDL3 2.0 +s_47343 RIMS4 2.0 +s_56575 THUMPD1 2.0 +s_3261 ARHGAP18 2.0 +s_8148 C6orf165 2.0 +s_17030 DUSP10 2.0 +s_56155 TEX101 2.0 +s_21191 FLI1 2.0 +s_50732 SIK1 2.0 +s_2914 APCDD1 2.0 +s_30717 LDB3 2.0 +s_4702 AXIN1 4.0 +s_21360 FNIP2 2.0 +s_54350 STEAP4 2.0 +s_57227 TMEM14A 4.0 +s_58177 TNIK 2.0 +s_7465 C20orf26 4.0 +s_17327 ECE2 2.0 +s_51639 SLC30A10 2.0 +s_4352 ATP5A1 2.0 +s_18616 ERCC8 2.0 +s_44043 PRIMA1 2.0 +s_36712 NELL2 2.0 +s_61348 VPS16 2.0 +s_2680 ANO4 2.0 +s_30437 LAMB2 2.0 +s_33742 MFSD12 2.0 +s_58796 TRHR 2.0 +s_52365 SLCO5A1 2.0 +s_41281 PEMT 2.0 +s_23427 GON4L 2.0 +s_13427 CPSF3L 2.0 +s_40193 PAPD7 2.0 +s_21543 FPGT 4.0 +s_16722 DPH2 2.0 +s_40078 PAIP2B 2.0 +s_60284 UBL5 2.0 +s_59936 TXNDC15 2.0 +s_31898 LRRTM4 2.0 +s_44833 PSMG1 4.0 +s_19552 FAM166B 2.0 +s_19478 FAM151A 2.0 +s_30185 KRTAP1-3 2.0 +s_61742 WDR45 2.0 +s_7252 C1orf212 2.0 +s_29507 KIF9 2.0 +s_2786 AP1G1 2.0 +s_21222 FLT1 2.0 +s_38408 NUP93 2.0 +s_60875 USP25 2.0 +s_39905 P2RX5 2.0 +s_54470 STOML1 2.0 +s_19064 EYA4 2.0 +s_41060 PDGFRL 2.0 +s_32049 LUC7L 2.0 +s_11837 CHRNA9 2.0 +s_64166 ZNF563 2.0 +s_11211 CENPK 2.0 +s_63097 ZFYVE21 2.0 +s_24757 HAUS4 2.0 +s_4190 ATG7 2.0 +s_48629 RTN4 2.0 +s_22880 GJB3 2.0 +s_44427 PRR7 2.0 +s_464 AC069154.2 2.0 +s_22093 GALC 2.0 +s_55367 TAPBP 2.0 +s_56672 TIMM22 2.0 +s_22286 GAS7 2.0 +s_45341 PVR 2.0 +s_34498 MPL 2.0 +s_60077 UBA7 6.0 +s_44215 PRMT5 2.0 +s_15576 DEFB125 2.0 +s_44098 PRKAR2B 6.0 +s_38270 NUDT19 2.0 +s_12662 CNNM3 2.0 +s_51149 SLC18A2 2.0 +s_42223 PKP4 2.0 +s_31072 LIMK1 2.0 +s_6339 C12orf53 2.0 +s_26400 HTR3E 2.0 +s_43315 PPARD 2.0 +s_28264 JAM3 2.0 +s_33927 MIER1 2.0 +s_11251 CEP104 2.0 +s_33388 MED24 2.0 +s_53844 SRGAP1 2.0 +s_40003 PACSIN2 2.0 +s_5428 BIK 2.0 +s_28459 KAZN 2.0 +s_12578 CNBP 2.0 +s_20731 FCRL3 2.0 +s_41692 PHKB 6.0 +s_13730 CRTC2 2.0 +s_50741 SIKE1 4.0 +s_10340 CD276 2.0 +s_42441 PLD6 2.0 +s_32600 MAP2K1 4.0 +s_21836 FXYD3 10.0 +s_33227 MCTP2 2.0 +s_23930 GPS1 2.0 +s_58948 TRIM46 2.0 +s_23579 GPER 2.0 +s_19158 FABP12 2.0 +s_26003 HPGD 2.0 +s_12701 CNOT7 2.0 +s_41164 PDS5B 2.0 +s_35675 MYLIP 2.0 +s_54071 SSX5 2.0 +s_59652 TTC9C 2.0 +s_35593 MYH10 2.0 +s_28060 ITGB1BP1 2.0 +s_52258 SLC8A3 4.0 +s_52898 SNX14 2.0 +s_25618 HMGCS1 2.0 +s_5068 BBS9 2.0 +s_4389 ATP5J 2.0 +s_49674 SEC62 2.0 +s_10264 CD1D 2.0 +s_20442 FBXL16 2.0 +s_11296 CEP41 2.0 +s_64923 ZSCAN22 2.0 +s_43954 PRDX3 2.0 +s_41735 PHOX2A 2.0 +s_33740 MFSD11 2.0 +s_2779 AP000892.1 2.0 +s_12703 CNOT7 2.0 +s_23338 GNMT 2.0 +s_14454 CXXC1 2.0 +s_49387 SCO1 2.0 +s_9124 CARD8 2.0 +s_42754 PML 4.0 +s_38814 OPRD1 2.0 +s_40024 PADI4 2.0 +s_29225 KIAA1147 2.0 +s_43402 PPID 2.0 +s_58669 TRAF3IP3 2.0 +s_59528 TTC17 2.0 +s_19114 F2RL3 2.0 +s_3339 ARHGAP35 2.0 +s_1522 AGPAT2 2.0 +s_33006 MBD2 2.0 +s_64149 ZNF558 2.0 +s_9791 CCDC69 2.0 +s_51442 SLC25A4 2.0 +s_59174 TRPC4 2.0 +s_37772 NQO2 2.0 +s_28649 KCNH8 2.0 +s_39896 P2RX3 2.0 +s_44644 PSG4 2.0 +s_51440 SLC25A39 2.0 +s_23954 GPSM3 2.0 +s_58911 TRIM36 2.0 +s_20632 FBXW12 2.0 +s_50149 SETMAR 2.0 +s_42606 PLK4 4.0 +s_55148 TAB1 2.0 +s_64628 ZNF772 2.0 +s_10616 CDC34 2.0 +s_38307 NUDT8 2.0 +s_23831 GPR35 2.0 +s_17055 DUSP15 2.0 +s_6922 C19orf44 2.0 +s_42494 PLEKHF2 2.0 +s_2104 ALPK1 2.0 +s_17640 EGFR 2.0 +s_37797 NR1H3 2.0 +s_23299 GNG3 2.0 +s_9517 CCDC125 2.0 +s_7562 C22orf42 2.0 +s_38149 NTNG1 2.0 +s_64633 ZNF774 2.0 +s_34420 MORN3 2.0 +s_56144 TET2 2.0 +s_18093 EMC6 2.0 +s_63835 ZNF410 2.0 +s_35521 MYBPC1 2.0 +s_64601 ZNF75D 2.0 +s_42105 PITX2 2.0 +s_39091 OR2M4 4.0 +s_1765 AKAP13 2.0 +s_6189 C11orf45 2.0 +s_63701 ZNF330 2.0 +s_28136 ITM2A 2.0 +s_56984 TMCO1 2.0 +s_49007 SAMSN1 2.0 +s_33654 METTL7A 4.0 +s_41626 PHF14 2.0 +s_34072 MLF1 2.0 +s_8880 CALR 2.0 +s_8738 CACNB4 2.0 +s_64012 ZNF496 2.0 +s_59206 TRPM3 2.0 +s_3971 ASIC5 2.0 +s_190 ABCC10 2.0 +s_41999 PIM1 2.0 +s_64465 ZNF684 2.0 +s_18728 ESD 2.0 +s_33786 MGA 2.0 +s_39611 OS9 2.0 +s_3484 ARID1B 2.0 +s_1238 ADH4 2.0 +s_53695 SPRTN 2.0 +s_23676 GPR126 2.0 +s_26052 HRAS 2.0 +s_36545 NDUFS1 2.0 +s_63208 ZMAT5 2.0 +s_2908 APC 2.0 +s_15119 DCAF8 2.0 +s_64395 ZNF655 2.0 +s_54556 STUB1 2.0 +s_10027 CCNC 2.0 +s_20178 FAM83C 2.0 +s_38266 NUDT17 2.0 +s_63517 ZNF233 2.0 +s_5435 BIN1 6.0 +s_13322 CPEB3 6.0 +s_19210 FAHD2A 2.0 +s_28276 JDP2 2.0 +s_38449 NXF1 2.0 +s_44619 PSEN1 2.0 +s_49290 SCMH1 2.0 +s_63232 ZMYM3 2.0 +s_47908 RP11-173D9.3 2.0 +s_51358 SLC25A18 2.0 +s_42513 PLEKHG5 2.0 +s_270 ABHD1 2.0 +s_58611 TPSG1 2.0 +s_45665 RAB33A 2.0 +s_35550 MYCL1 2.0 +s_55953 TCTN3 2.0 +s_39190 OR4D5 2.0 +s_64862 ZP2 2.0 +s_48451 RRM2 2.0 +s_44136 PRKCZ 2.0 +s_12532 CMTM1 2.0 +s_13958 CSPP1 2.0 +s_61437 VSIG1 2.0 +s_2427 ANKH 2.0 +s_48236 RPP25 2.0 +s_25248 HHIP 2.0 +s_49666 SEC61A2 4.0 +s_40916 PDE1C 2.0 +s_51267 SLC22A3 4.0 +s_45250 PTPRU 2.0 +s_54454 STMN2 2.0 +s_50448 SH3BP5 2.0 +s_35505 MYB 2.0 +s_34174 MMD2 2.0 +s_43046 POLR1D 2.0 +s_26919 IGSF1 2.0 +s_59350 TSKU 2.0 +s_52462 SMAD3 2.0 +s_44496 PRSS22 2.0 +s_12310 CLIC1 2.0 +s_60920 USP38 2.0 +s_42557 PLEKHO2 2.0 +s_37636 NPEPL1 2.0 +s_56222 TFAP2A 2.0 +s_46417 RBM22 2.0 +s_20477 FBXL6 2.0 +s_30504 LAPTM4A 2.0 +s_49873 4-Sep 2.0 +s_22231 GAPDH 2.0 +s_24866 HCRT 2.0 +s_26084 HRH4 2.0 +s_266 ABCG8 2.0 +s_31387 LPCAT1 2.0 +s_38114 NTF3 2.0 +s_13990 CST11 2.0 +s_24036 GRB14 2.0 +s_50585 SHISA4 2.0 +s_14163 CTNNA1 2.0 +s_1729 AK2 2.0 +s_62985 ZFHX3 2.0 +s_21318 FNBP1L 2.0 +s_13575 CREBRF 2.0 +s_5344 BET1 2.0 +s_49424 SCRN2 2.0 +s_31170 LIPN 2.0 +s_54781 SURF2 2.0 +s_51325 SLC25A1 2.0 +s_34136 MLNR 2.0 +s_31677 LRRC31 2.0 +s_53307 SPARCL1 2.0 +s_28022 ITGA7 2.0 +s_31356 LOXL3 2.0 +s_118 ABCA12 2.0 +s_12481 CLUL1 2.0 +s_40393 PAX3 2.0 +s_39614 OS9 2.0 +s_22342 GBA2 2.0 +s_1136 ADC 2.0 +s_10401 CD37 2.0 +s_4512 ATP7A 2.0 +s_10615 CDC27 2.0 +s_54497 STOX1 2.0 +s_46754 REG4 2.0 +s_20299 FAP 2.0 +s_63316 ZNF138 2.0 +s_42213 PKP2 2.0 +s_52161 SLC6A4 2.0 +s_60954 USP48 2.0 +s_14721 CYP2C9 2.0 +s_54067 SSX3 2.0 +s_42512 PLEKHG5 2.0 +s_32324 MAD2L1BP 2.0 +s_26149 HSD11B1L 2.0 +s_62941 ZFAND1 2.0 +s_306 ABHD16A 2.0 +s_42173 PKIG 2.0 +s_33499 MEOX1 2.0 +s_2639 ANKS1A 2.0 +s_9221 CASP4 4.0 +s_60951 USP48 2.0 +s_42487 PLEKHB2 2.0 +s_12463 CLTB 2.0 +s_17140 DYDC2 2.0 +s_15238 DCTD 2.0 +s_32766 MAPK8IP3 2.0 +s_6844 C18orf1 2.0 +s_29768 KLHL25 2.0 +s_58192 TNIP3 2.0 +s_26239 HSF4 2.0 +s_14209 CTRL 2.0 +s_7539 C22orf25 2.0 +s_21263 FMNL3 2.0 +s_56798 TLK1 2.0 +s_30163 KRT80 2.0 +s_28530 KCNAB1 2.0 +s_50079 SESN2 2.0 +s_17622 EGFL7 2.0 +s_27107 IL17RE 2.0 +s_61128 VASH2 2.0 +s_7629 C2orf44 2.0 +s_59045 TRIML2 2.0 +s_53186 SP110 2.0 +s_44696 PSMA8 2.0 +s_4081 ATAT1 2.0 +s_59776 TUBA3C 2.0 +s_26981 IKBKB 2.0 +s_11984 CINP 2.0 +s_38231 NUDT1 2.0 +s_34096 MLKL 2.0 +s_39703 OSM 2.0 +s_44761 PSMC4 2.0 +s_29844 KLK1 2.0 +s_46470 RBM43 2.0 +s_21735 FTSJ1 2.0 +s_54159 ST7L 2.0 +s_29161 KIAA0586 2.0 +s_62066 WNT11 2.0 +s_32768 MAPK9 2.0 +s_38834 OPTC 2.0 +s_27041 IL12RB2 2.0 +s_25301 HIGD1C 2.0 +s_48626 RTN4 2.0 +s_2191 AMBRA1 2.0 +s_64637 ZNF775 2.0 +s_24425 GTF2IRD1 4.0 +s_28025 ITGA7 2.0 +s_21739 FTSJ2 2.0 +s_56140 TET1 2.0 +s_18340 EOGT 2.0 +s_48335 RPS6KA1 2.0 +s_8918 CAMK2N1 2.0 +s_9126 CARD8 2.0 +s_34993 MSC 2.0 +s_62519 YY1AP1 2.0 +s_17754 EIF2B2 2.0 +s_3894 ASB7 2.0 +s_1366 ADRBK2 2.0 +s_63368 ZNF169 2.0 +s_33217 MCRS1 2.0 +s_791 ACSS3 2.0 +s_3070 APOL5 2.0 +s_158 ABCB4 2.0 +s_46169 RASAL2 2.0 +s_31573 LRP3 2.0 +s_15806 DGKQ 2.0 +s_3426 ARHGEF2 2.0 +s_22505 GDAP2 2.0 +s_43731 PPP4R4 2.0 +s_62463 YPEL3 2.0 +s_1351 ADRA2A 2.0 +s_58570 TPPP 2.0 +s_27563 INPP5K 2.0 +s_64662 ZNF783 2.0 +s_43701 PPP2R5D 2.0 +s_41032 PDE9A 2.0 +s_40077 PAIP2B 2.0 +s_55106 SYTL2 2.0 +s_36104 NAT1 2.0 +s_5659 BPIFA2 2.0 +s_24738 HAS3 2.0 +s_23688 GPR135 2.0 +s_44125 PRKCI 2.0 +s_42154 PKDCC 2.0 +s_52320 SLC9B2 2.0 +s_56287 TFF1 2.0 +s_26218 HSDL1 2.0 +s_48811 S100A14 2.0 +s_27403 IMMT 2.0 +s_44547 PRSS50 2.0 +s_13554 CREB3L3 2.0 +s_52812 SNRNP35 2.0 +s_9678 CCDC28B 2.0 +s_42982 POLD4 2.0 +s_9038 CAPN3 2.0 +s_24550 GYG1 2.0 +s_7927 C4orf19 2.0 +s_59893 TWF2 2.0 +s_21776 FUS 2.0 +s_38699 OLA1 2.0 +s_15466 DDX54 2.0 +s_57105 TMEM110 2.0 +s_47396 RIPPLY2 2.0 +s_29679 KLHDC3 2.0 +s_19864 FAM214B 2.0 +s_22859 GIT2 2.0 +s_63818 ZNF397 2.0 +s_62767 ZC3HAV1 2.0 +s_30390 LAD1 2.0 +s_54683 SULT1C3 2.0 +s_29008 KDM5D 2.0 +s_24721 HARS 2.0 +s_19875 FAM217A 2.0 +s_33598 METTL18 2.0 +s_43299 PPAPDC1B 2.0 +s_23606 GPM6A 2.0 +s_8917 CAMK2G 2.0 +s_7803 C3orf22 2.0 +s_52734 SNAP91 4.0 +s_46558 RBPJL 2.0 +s_44462 PRRT2 2.0 +s_30938 LHB 2.0 +s_33858 MIA2 2.0 +s_1394 AEN 2.0 +s_39870 OXSR1 2.0 +s_4906 BAG6 2.0 +s_16155 DLK2 2.0 +s_35274 MTMR4 2.0 +s_10518 CD81 2.0 +s_39057 OR2F2 2.0 +s_43913 PRDM16 2.0 +s_34638 MRPL1 2.0 +s_612 ACER3 2.0 +s_32740 MAPK3 2.0 +s_16130 DLGAP1 2.0 +s_15564 DEFB119 2.0 +s_41047 PDGFC 2.0 +s_30824 LEPRE1 2.0 +s_19702 FAM189B 2.0 +s_16740 DPM3 2.0 +s_13557 CREB3L4 2.0 +s_10008 CCNA1 2.0 +s_58486 TP73 2.0 +s_18717 ESAM 2.0 +s_63612 ZNF280D 2.0 +s_14187 CTNND2 2.0 +s_59449 TSPO2 2.0 +s_42709 PLXNB3 2.0 +s_39221 OR4M2 2.0 +s_49750 SEMA3F 2.0 +s_8476 C9orf3 2.0 +s_45561 RAB11A 2.0 +s_5542 BMP5 2.0 +s_1064 ADAMTS4 2.0 +s_5354 BET3L 2.0 +s_17631 EGFLAM 2.0 +s_36593 NEBL 2.0 +s_6085 C10orf2 2.0 +s_13428 CPSF3L 2.0 +s_25023 HECW1 2.0 +s_3641 ARMC9 2.0 +s_56315 TFPT 2.0 +s_3278 ARHGAP22 2.0 +s_49946 SERPINA1 2.0 +s_20760 FDFT1 2.0 +s_26065 HRCT1 2.0 +s_50473 SH3GL1 2.0 +s_22971 GLI1 2.0 +s_24638 H6PD 2.0 +s_40488 PCDH11X 2.0 +s_61210 VEGFB 2.0 +s_28841 KCNQ5 2.0 +s_43717 PPP3R1 2.0 +s_25342 HIRA 2.0 +s_57951 TMPRSS4 2.0 +s_34011 MITF 2.0 +s_54412 STK32B 2.0 +s_16037 DISC1 2.0 +s_51701 SLC34A3 2.0 +s_54291 STAT4 2.0 +s_24419 GTF2I 2.0 +s_45973 RALB 2.0 +s_28705 KCNJ6 2.0 +s_5581 BNIP1 2.0 +s_19856 FAM213A 2.0 +s_18308 ENTPD1 2.0 +s_59198 TRPM1 2.0 +s_21871 FZD10 2.0 +s_1850 AKR1C4 2.0 +s_6867 C18orf54 2.0 +s_35715 MYO18B 2.0 +s_22242 GAPVD1 2.0 +s_32713 MAP7D3 2.0 +s_49953 SERPINA12 2.0 +s_55916 TCP11 2.0 +s_56174 TEX19 2.0 +s_22072 GAL 2.0 +s_41033 PDE9A 2.0 +s_26471 HYAL3 2.0 +s_60244 UBE2Z 2.0 +s_12589 CNEP1R1 2.0 +s_29896 KLK8 2.0 +s_29769 KLHL26 2.0 +s_39346 OR5AP2 2.0 +s_15213 DCPS 2.0 +s_48577 RTBDN 2.0 +s_32146 LYAR 2.0 +s_26382 HTR3C 2.0 +s_33001 MBD1 2.0 +s_41972 PIK3R2 2.0 +s_33212 MCOLN3 2.0 +s_35423 MUL1 2.0 +s_7838 C3orf35 2.0 +s_51092 SLC16A4 2.0 +s_20336 FASTK 2.0 +s_33469 MEI1 2.0 +s_5549 BMP7 2.0 +s_2490 ANKRD16 2.0 +s_38674 OGFRL1 2.0 +s_26322 HSPBAP1 2.0 +s_31244 LMNA 2.0 +s_34063 MLC1 2.0 +s_15550 DEFB113 2.0 +s_52892 SNX12 2.0 +s_25799 HOOK2 2.0 +s_55486 TAX1BP1 2.0 +s_4351 ATP5A1 2.0 +s_49917 SERHL2 2.0 +s_46614 RCHY1 2.0 +s_62680 ZBTB7B 2.0 +s_49488 SDCBP 2.0 +s_21866 FYTTD1 2.0 +s_23092 GLTPD1 2.0 +s_10675 CDC73 2.0 +s_12764 CNTN2 2.0 +s_9223 CASP5 2.0 +s_38310 NUDT8 2.0 +s_7059 C1QTNF9B 2.0 +s_33162 MCM3AP 2.0 +s_8498 C9orf50 2.0 +s_16876 DSC1 2.0 +s_14370 CWH43 2.0 +s_22565 GDPD1 2.0 +s_4304 ATP1B4 2.0 +s_3600 ARMC10 2.0 +s_18120 EMID1 2.0 +s_21865 FYN 2.0 +s_60042 U2SURP 2.0 +s_13930 CSNK1G3 2.0 +s_6618 C16orf53 2.0 +s_26173 HSD17B12 2.0 +s_46035 RANBP3L 2.0 +s_13167 CORO2A 2.0 +s_10481 CD6 2.0 +s_4563 ATPIF1 2.0 +s_50071 SERTAD4 2.0 +s_39089 OR2M3 2.0 +s_58390 TOR1AIP2 2.0 +s_45132 PTPN2 2.0 +s_34536 MPPED2 2.0 +s_24336 GSTM5 2.0 +s_38670 OGFR 2.0 +s_4606 ATXN3 2.0 +s_5049 BBS12 2.0 +s_28134 ITM2A 2.0 +s_23612 GPN1 2.0 +s_16085 DLEC1 2.0 +s_2525 ANKRD28 2.0 +s_1792 AKAP7 2.0 +s_27701 IPO11 2.0 +s_25633 HMGN5 2.0 +s_33287 MDM4 2.0 +s_17847 EIF4E 2.0 +s_58327 TOMM34 2.0 +s_54101 ST3GAL3 2.0 +s_41507 PGLYRP3 2.0 +s_38705 OLAH 2.0 +s_7336 C1orf61 2.0 +s_34439 MOSPD3 2.0 +s_33343 MED12 2.0 +s_30145 KRT75 2.0 +s_7793 C3orf18 2.0 +s_13874 CSH2 2.0 +s_14274 CTTN 2.0 +s_38166 NTRK2 2.0 +s_2916 APCDD1L 2.0 +s_41582 PHB 2.0 +s_16033 DISC1 2.0 +s_54156 ST7L 2.0 +s_21942 GABARAPL1 2.0 +s_19312 FAM115C 2.0 +s_5431 BIN1 2.0 +s_44378 PRR15 2.0 +s_22113 GALNT1 2.0 +s_11744 CHN1 2.0 +s_13702 CROT 2.0 +s_14052 CT62 2.0 +s_28143 ITM2C 2.0 +s_43456 PPM1B 2.0 +s_1396 AES 2.0 +s_21931 GAB2 2.0 +s_39536 OR8J3 2.0 +s_62622 ZBTB37 2.0 +s_10417 CD3G 2.0 +s_23789 GPR176 2.0 +s_37011 NICN1 2.0 +s_55412 TAS1R2 2.0 +s_36626 NEDD4L 2.0 +s_62812 ZCCHC4 2.0 +s_18097 EMC7 2.0 +s_36145 NAV2 2.0 +s_18994 EXOG 2.0 +s_61047 UTY 2.0 +s_57912 TMPRSS11B 2.0 +s_56577 THUMPD1 2.0 +s_8419 C9orf123 2.0 +s_36127 NAT9 2.0 +s_57557 TMEM240 2.0 +s_36157 NBEA 2.0 +s_16271 DMRTA2 2.0 +s_44643 PSG4 2.0 +s_53557 SPINK8 2.0 +s_36256 NCF4 2.0 +s_46280 RASSF6 2.0 +s_47580 RNF141 2.0 +s_8514 C9orf71 2.0 +s_62629 ZBTB4 2.0 +s_4286 ATP1A3 2.0 +s_36001 NAGK 2.0 +s_38778 OPA3 2.0 +s_8907 CAMK2A 2.0 +s_10448 CD5 2.0 +s_20085 FAM69B 2.0 +s_31389 LPCAT1 2.0 +s_56204 TEX34 2.0 +s_30139 KRT72 2.0 +s_34962 MS4A6A 2.0 +s_12886 COL17A1 2.0 +s_46458 RBM4 2.0 +s_37813 NR1I3 2.0 +s_10007 CCNA1 0 +s_10164 CCS 0 +s_10200 CCT7 0 +s_10232 CD164 0 +s_1035 ADAMTS14 0 +s_10381 CD300LG 0 +s_10402 CD37 0 +s_10405 CD38 0 +s_10408 CD3D 0 +s_10425 CD40 0 +s_10434 CD44 0 +s_10437 CD46 0 +s_10541 CD8B 0 +s_10563 CD99L2 0 +s_10582 CDC14B 0 +s_10594 CDC20B 0 +s_10657 CDC42SE2 0 +s_10658 CDC42SE2 0 +s_10785 CDH3 0 +s_10943 CDKL5 0 +s_1101 ADAMTSL4 0 +s_11025 CDSN 0 +s_11054 CEACAM1 0 +s_1113 ADAR 0 +s_11153 CELF4 0 +s_1116 ADARB1 0 +s_11218 CENPL 0 +s_11222 CENPM 0 +s_1127 ADAT2 0 +s_11294 CEP41 0 +s_11317 CEP63 0 +s_11456 CFH 0 +s_11585 CHD1 0 +s_11598 CHD3 0 +s_11692 CHL1 0 +s_1177 ADCY3 0 +s_1179 ADCY4 0 +s_1183 ADCY5 0 +s_11877 CHST13 0 +s_11928 CHUK 0 +s_12015 CITED1 0 +s_12019 CIZ1 0 +s_12021 CIZ1 0 +s_12049 CKLF-CMTM1 0 +s_12057 CKMT2 0 +s_12082 CLCC1 0 +s_12089 CLCF1 0 +s_1212 ADD1 0 +s_12120 CLCN7 0 +s_12121 CLCN7 0 +s_12138 CLDN10 0 +s_12140 CLDN10 0 +s_12177 CLDN2 0 +s_12187 CLDN25 0 +s_12203 CLDND1 0 +s_12209 CLDND2 0 +s_12420 CLPTM1 0 +s_12425 CLPX 0 +s_12433 CLRN2 0 +s_12522 CMPK2 0 +s_12576 CNBP 0 +s_12611 CNGB1 0 +s_12624 CNIH2 0 +s_12666 CNNM3 0 +s_12708 CNP 0 +s_12856 COG8 0 +s_12875 COL14A1 0 +s_12906 COL22A1 0 +s_12923 COL27A1 0 +s_13026 COLEC12 0 +s_13035 COMMD1 0 +s_13067 COMT 0 +s_13091 COPG1 0 +s_13123 COQ2 0 +s_13198 COX11 0 +s_13220 COX4I2 0 +s_13253 COX7A2L 0 +s_13287 CPA5 0 +s_13290 CPA6 0 +s_13309 CPE 0 +s_13328 CPED1 0 +s_13338 CPLX3 0 +s_13387 CPO 0 +s_13389 CPO 0 +s_13393 CPOX 0 +s_13405 CPS1 0 +s_13486 CR2 0 +s_13512 CRB1 0 +s_1357 ADRB1 0 +s_13579 CREBZF 0 +s_13662 CRK 0 +s_13686 CRMP1 0 +s_13718 CRTAM 0 +s_13755 CRYBA1 0 +s_13856 CSF3 0 +s_13857 CSF3 0 +s_13879 CSHL1 0 +s_1393 AEN 0 +s_13937 CSNK2A1 0 +s_13985 CSRP3 0 +s_14021 CSTA 0 +s_14099 CTCFL 0 +s_14107 CTD-2616J11.4 0 +s_14153 CTIF 0 +s_14189 CTNND2 0 +s_14226 CTSC 0 +s_14286 CTU2 0 +s_14338 CUTA 0 +s_14364 CWF19L1 0 +s_14369 CWH43 0 +s_14418 CXCL3 0 +s_14425 CXCL6 0 +s_14439 CXCR4 0 +s_14463 CXXC4 0 +s_14467 CXXC5 0 +s_1450 AGA 0 +s_14520 CXorf61 0 +s_14586 CYBA 0 +s_14670 CYP26A1 0 +s_14761 CYP3A4 0 +s_14894 DAB2IP 0 +s_14938 DALRD3 0 +s_14995 DAXX 0 +s_14996 DAXX 0 +s_15017 DBF4 0 +s_15052 DBP 0 +s_15113 DCAF6 0 +s_15182 DCLRE1A 0 +s_15320 DDI1 0 +s_15363 DDX17 0 +s_15385 DDX23 0 +s_15405 DDX31 0 +s_15438 DDX46 0 +s_15440 DDX47 0 +s_15472 DDX58 0 +s_15482 DDX6 0 +s_15488 DDX60L 0 +s_1549 AGPS 0 +s_1550 AGPS 0 +s_15520 DEF8 0 +s_15522 DEF8 0 +s_15563 DEFB119 0 +s_15566 DEFB119 0 +s_15586 DEFB127 0 +s_15648 DENND2D 0 +s_15655 DENND4A 0 +s_15679 DEPDC1 0 +s_15700 DERL1 0 +s_15731 DFFB 0 +s_15800 DGKI 0 +s_15867 DHRS3 0 +s_15897 DHX16 0 +s_15939 DHX40 0 +s_15965 DIAPH3 0 +s_15988 DIO1 0 +s_1599 AGXT2L1 0 +s_1609 AHCY 0 +s_16149 DLGAP5 0 +s_16175 DLX1 0 +s_16190 DLX3 0 +s_16294 DMXL2 0 +s_16341 DNAH9 0 +s_16417 DNAJC13 0 +s_16505 DNALI1 0 +s_16506 DNALI1 0 +s_16554 DNM2 0 +s_16577 DNMT3A 0 +s_16607 DOCK3 0 +s_1661 AIF1 0 +s_16629 DOCK8 0 +s_1663 AIF1L 0 +s_16675 DOPEY1 0 +s_16745 DPP10 0 +s_16798 DPYD 0 +s_16866 DRGX 0 +s_16867 DRGX 0 +s_1687 AIM1 0 +s_16878 DSC1 0 +s_16993 DUOX1 0 +s_17119 DUT 0 +s_17168 DYNC2LI1 0 +s_17195 DYRK1B 0 +s_17214 DYX1C1 0 +s_17224 DZIP1L 0 +s_17229 E2F1 0 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RIPPLY1 0 +s_47413 RLBP1 0 +s_47554 RNF130 0 +s_47584 RNF144A 0 +s_47594 RNF145 0 +s_47622 RNF165 0 +s_47710 RNF215 0 +s_47777 RNF44 0 +s_47780 RNF6 0 +s_47786 RNF7 0 +s_47791 RNF8 0 +s_47915 RP11-178D12.1 0 +s_47946 RP11-428C6.1 0 +s_47969 RP11-6F2.7 0 +s_47970 RP11-6F2.7 0 +s_48013 RP4-697K14.7 0 +s_48066 RPAP3 0 +s_48073 RPE 0 +s_48097 RPH3AL 0 +s_48098 RPH3AL 0 +s_48179 RPL36 0 +s_48201 RPL6 0 +s_4837 B4GALT5 0 +s_48399 RPUSD2 0 +s_4841 B4GALT6 0 +s_48414 RQCD1 0 +s_4843 B4GALT7 0 +s_48438 RREB1 0 +s_48461 RRNAD1 0 +s_48488 RRS1 0 +s_48512 RSC1A1 0 +s_4868 BACE1 0 +s_48714 RUSC1 0 +s_48860 S100B 0 +s_48874 S100Z 0 +s_48933 SALL3 0 +s_4898 BAG4 0 +s_49069 SASS6 0 +s_49192 SCARB1 0 +s_49246 SCGB1D1 0 +s_4925 BAIAP2 0 +s_49278 SCIN 0 +s_49297 SCML1 0 +s_49354 SCN7A 0 +s_49570 SDR9C7 0 +s_49599 SEC14L2 0 +s_49625 SEC22A 0 +s_49651 SEC24D 0 +s_49668 SEC61A2 0 +s_49706 SELE 0 +s_4972 BARHL2 0 +s_49775 SEMA4F 0 +s_49799 SEMA6D 0 +s_49844 SEPP1 0 +s_49859 12-Sep 0 +s_49881 5-Sep 0 +s_49934 SERINC5 0 +s_49957 SERPINA3 0 +s_50004 SERPINB5 0 +s_5001 BAX 0 +s_5006 BAZ1A 0 +s_50112 SETD3 0 +s_50123 SETD6 0 +s_50127 SETD7 0 +s_50162 SEZ6L2 0 +s_5022 BAZ2B 0 +s_5026 BBC3 0 +s_50280 SGCA 0 +s_50284 SGCB 0 +s_50342 SGPP2 0 +s_50388 SH2D3C 0 +s_50391 SH2D3C 0 +s_50491 SH3KBP1 0 +s_505 ACACB 0 +s_50517 SH3TC2 0 +s_5056 BBS4 0 +s_50560 SHE 0 +s_50596 SHISA6 0 +s_50652 SI 0 +s_50684 SIGLEC1 0 +s_50692 SIGLEC10 0 +s_50693 SIGLEC11 0 +s_50722 SIGLEC9 0 +s_50761 SIPA1 0 +s_50779 SIRPB1 0 +s_50780 SIRPB1 0 +s_51043 SLC15A1 0 +s_51096 SLC16A5 0 +s_51179 SLC1A2 0 +s_51276 SLC22A5 0 +s_51312 SLC24A4 0 +s_51344 SLC25A13 0 +s_51482 SLC25A5 0 +s_51528 SLC26A9 0 +s_51555 SLC28A1 0 +s_51613 SLC2A6 0 +s_51660 SLC30A6 0 +s_51715 SLC35A4 0 +s_51729 SLC35B3 0 +s_51774 SLC35F3 0 +s_51783 SLC35G2 0 +s_51872 SLC39A14 0 +s_51904 SLC39A8 0 +s_52017 SLC4A2 0 +s_52093 SLC5A5 0 +s_52206 SLC7A14 0 +s_52255 SLC8A2 0 +s_52313 SLC9B1 0 +s_52364 SLCO4C1 0 +s_52383 SLFN13 0 +s_52421 SLITRK4 0 +s_52435 SLMO1 0 +s_52485 SMAP1 0 +s_5253 BCO2 0 +s_52574 SMCR8 0 +s_52587 SMG5 0 +s_52601 SMG7 0 +s_52617 SMO 0 +s_52642 SMPD4 0 +s_5268 BDH1 0 +s_52758 SNAPIN 0 +s_52784 SNIP1 0 +s_52787 SNIP1 0 +s_52833 SNRPB2 0 +s_52989 SNX8 0 +s_53 AAK1 0 +s_53048 SON 0 +s_53055 SORBS1 0 +s_53109 SOSTDC1 0 +s_53151 SOX30 0 +s_53153 SOX30 0 +s_53181 SP100 0 +s_53438 SPDYC 0 +s_53476 SPERT 0 +s_53512 SPI1 0 +s_53525 SPIN1 0 +s_53535 SPINK1 0 +s_53555 SPINK6 0 +s_53574 SPINT1 0 +s_53639 SPP1 0 +s_53691 SPRR3 0 +s_53740 SPTA1 0 +s_53830 SREK1 0 +s_53993 SSBP1 0 +s_54019 SSPN 0 +s_54054 SSTR5 0 +s_54078 ST14 0 +s_54092 ST3GAL3 0 +s_54099 ST3GAL3 0 +s_54292 STAT5A 0 +s_54305 STATH 0 +s_54314 STAU2 0 +s_54327 STC2 0 +s_5437 BIN2 0 +s_54380 STK17A 0 +s_54403 STK3 0 +s_54480 STON1 0 +s_54588 STX5 0 +s_54609 STXBP4 0 +s_54639 SUCLG1 0 +s_54645 SUCNR1 0 +s_54679 SULT1B1 0 +s_54684 SULT1C3 0 +s_54704 SULT2B1 0 +s_54758 SUPT4H1 0 +s_54772 SUPV3L1 0 +s_54801 SUSD4 0 +s_54866 SWT1 0 +s_5492 BLOC1S3 0 +s_54942 SYNDIG1 0 +s_5503 BMF 0 +s_55131 SZT2 0 +s_55147 TAAR8 0 +s_55187 TACO1 0 +s_55464 TAS2R8 0 +s_55509 TBC1D10C 0 +s_55520 TBC1D14 0 +s_55528 TBC1D15 0 +s_55577 TBC1D30 0 +s_55709 TBX21 0 +s_55725 TBX5 0 +s_55844 TCF4 0 +s_55845 TCF4 0 +s_55862 TCF7L2 0 +s_55868 TCHH 0 +s_5588 BNIP2 0 +s_55911 TCP10L2 0 +s_55913 TCP11 0 +s_55922 TCP11L2 0 +s_55946 TCTN1 0 +s_56006 TEAD2 0 +s_56014 TEAD4 0 +s_56080 TEN1 0 +s_56099 TERF1 0 +s_56118 TES 0 +s_56167 TEX13B 0 +s_5618 BOK 0 +s_56207 TEX9 0 +s_56284 TFEC 0 +s_56297 TFG 0 +s_56361 TGFBR2 0 +s_56373 TGIF1 0 +s_56415 TGS1 0 +s_56492 THEM4 0 +s_56509 THNSL1 0 +s_5655 BPIFA1 0 +s_56621 TIFA 0 +s_56646 TIMD4 0 +s_56684 TIMM8B 0 +s_56805 TLL1 0 +s_56819 TLR10 0 +s_56826 TLR3 0 +s_56873 TM4SF18 0 +s_57016 TMED10 0 +s_57082 TMEM106C 0 +s_57087 TMEM107 0 +s_57150 TMEM127 0 +s_57173 TMEM132B 0 +s_57181 TMEM132E 0 +s_57189 TMEM134 0 +s_57288 TMEM164 0 +s_57299 TMEM167B 0 +s_57409 TMEM194A 0 +s_57422 TMEM198 0 +s_57429 TMEM2 0 +s_57475 TMEM212 0 +s_57531 TMEM231 0 +s_57568 TMEM245 0 +s_57700 TMEM54 0 +s_57873 TMF1 0 +s_57992 TMUB1 0 +s_58180 TNIP1 0 +s_58211 TNKS2 0 +s_58237 TNNT1 0 +s_58256 TNPO2 0 +s_58259 TNPO3 0 +s_58309 TOM1 0 +s_58485 TP73 0 +s_58503 TPD52 0 +s_58533 TPI1 0 +s_5857 BSPRY 0 +s_58612 TPSG1 0 +s_58633 TRA2B 0 +s_58655 TRAF3 0 +s_58668 TRAF3IP2 0 +s_58690 TRAK1 0 +s_58809 TRIB2 0 +s_58962 TRIM50 0 +s_58968 TRIM52 0 +s_59050 TRIO 0 +s_59107 TRMT1L 0 +s_59133 TRMT61B 0 +s_59160 TROVE2 0 +s_59173 TRPC4 0 +s_59196 TRPM1 0 +s_59204 TRPM3 0 +s_59311 TSEN54 0 +s_59332 TSHB 0 +s_59340 TSHZ2 0 +s_59360 TSNARE1 0 +s_5952 BTG4 0 +s_59539 TTC21A 0 +s_59602 TTC39A 0 +s_59654 TTC9C 0 +s_59717 TTLL6 0 +s_5974 BTN3A1 0 +s_59748 TTYH1 0 +s_59807 TUBB2B 0 +s_59859 TULP1 0 +s_59870 TULP3 0 +s_59955 TXNDC8 0 +s_59983 TXNRD2 0 +s_600 ACE 0 +s_60169 UBE2H 0 +s_60209 UBE2Q2 0 +s_60237 UBE2V2 0 +s_60248 UBE3A 0 +s_60250 UBE3B 0 +s_60373 UBXN6 0 +s_60396 UCKL1 0 +s_60423 UEVLD 0 +s_60438 UFSP1 0 +s_60449 UGDH 0 +s_60517 UGT2A1 0 +s_60542 UGT3A1 0 +s_60603 UMODL1 0 +s_60614 UNC119 0 +s_60649 UNC5B 0 +s_6068 C10orf125 0 +s_6071 C10orf128 0 +s_60753 UQCRC2 0 +s_60780 URM1 0 +s_60839 USP15 0 +s_60851 USP19 0 +s_60925 USP4 0 +s_6100 C10orf53 0 +s_6106 C10orf54 0 +s_61149 VAV2 0 +s_61173 VCAM1 0 +s_61178 VCAN 0 +s_61221 VEPH1 0 +s_61263 VIL1 0 +s_61341 VPS13C 0 +s_61344 VPS13D 0 +s_61367 VPS29 0 +s_61529 VWA5A 0 +s_61531 VWA5A 0 +s_61587 WBP1 0 +s_61595 WBP2 0 +s_61623 WDFY1 0 +s_61640 WDHD1 0 +s_61662 WDR16 0 +s_61695 WDR26 0 +s_61739 WDR44 0 +s_6200 C11orf49 0 +s_62019 WISP1 0 +s_62098 WNT5B 0 +s_62114 WNT8A 0 +s_62171 WTAP 0 +s_62249 XKR3 0 +s_62257 XKR6 0 +s_62275 XPC 0 +s_62320 XRCC4 0 +s_62361 YAE1D1 0 +s_62550 ZBBX 0 +s_62559 ZBED6 0 +s_62567 ZBTB1 0 +s_62624 ZBTB37 0 +s_62657 ZBTB47 0 +s_62759 ZC3H7A 0 +s_62845 ZDHHC11 0 +s_62862 ZDHHC16 0 +s_62881 ZDHHC2 0 +s_6292 C12orf23 0 +s_62975 ZFC3H1 0 +s_63034 ZFP64 0 +s_63104 ZFYVE27 0 +s_63107 ZFYVE27 0 +s_63114 ZFYVE28 0 +s_63217 ZMIZ2 0 +s_63228 ZMYM3 0 +s_63234 ZMYM3 0 +s_6326 C12orf49 0 +s_63302 ZNF132 0 +s_63362 ZNF167 0 +s_63435 ZNF200 0 +s_63487 ZNF223 0 +s_63594 ZNF276 0 +s_636 ACO1 0 +s_63746 ZNF354B 0 +s_63755 ZNF362 0 +s_6376 C12orf74 0 +s_63903 ZNF436 0 +s_63905 ZNF438 0 +s_63923 ZNF442 0 +s_63934 ZNF445 0 +s_63935 ZNF446 0 +s_63964 ZNF469 0 +s_63983 ZNF480 0 +s_6409 C14orf105 0 +s_64137 ZNF554 0 +s_64241 ZNF586 0 +s_6427 C14orf133 0 +s_64356 ZNF639 0 +s_64393 ZNF655 0 +s_64396 ZNF655 0 +s_64419 ZNF668 0 +s_64424 ZNF669 0 +s_64459 ZNF682 0 +s_64479 ZNF688 0 +s_64581 ZNF746 0 +s_64627 ZNF772 0 +s_64638 ZNF776 0 +s_64652 ZNF780A 0 +s_64791 ZNF85 0 +s_64851 ZNRF3 0 +s_64871 ZPBP 0 +s_64878 ZPLD1 0 +s_64898 ZSCAN10 0 +s_64930 ZSCAN30 0 +s_64997 ZYG11A 0 +s_6525 C15orf39 0 +s_6592 C16orf13 0 +s_6639 C16orf62 0 +s_6707 C17orf102 0 +s_6710 C17orf104 0 +s_6728 C17orf112 0 +s_6736 C17orf39 0 +s_6794 C17orf72 0 +s_6814 C17orf80 0 +s_6849 C18orf21 0 +s_6859 C18orf32 0 +s_6862 C18orf34 0 +s_6906 C19orf38 0 +s_7053 C1QTNF7 0 +s_7128 C1orf122 0 +s_7144 C1orf130 0 +s_7162 C1orf144 0 +s_7234 C1orf198 0 +s_7341 C1orf63 0 +s_747 ACSL1 0 +s_76 AARS2 0 +s_7674 C2orf57 0 +s_7681 C2orf62 0 +s_7692 C2orf63 0 +s_77 AARSD1 0 +s_78 AARSD1 0 +s_781 ACSS1 0 +s_786 ACSS2 0 +s_7940 C4orf26 0 +s_7970 C4orf37 0 +s_8000 C4orf52 0 +s_804 ACTB 0 +s_8073 C5orf51 0 +s_8141 C6orf162 0 +s_8227 C7orf10 0 +s_8281 C7orf59 0 +s_8318 C8A 0 +s_8403 C9orf100 0 +s_8470 C9orf24 0 +s_8699 CACNA1G 0 +s_8705 CACNA1I 0 +s_871 ACTR8 0 +s_874 ACTR8 0 +s_8757 CACNG5 0 +s_8797 CADPS 0 +s_8879 CALR 0 +s_8910 CAMK2B 0 +s_893 ACVR1B 0 +s_8930 CAMKK1 0 +s_8954 CAMSAP1 0 +s_9064 CAPRIN1 0 +s_9077 CAPSL 0 +s_9109 CARD17 0 +s_913 ACY1 0 +s_9171 CASD1 0 +s_9196 CASP10 0 +s_9285 CATSPER3 0 +s_9506 CCDC120 0 +s_9507 CCDC121 0 +s_952 ADAM12 0 +s_9584 CCDC149 0 +s_964 ADAM18 0 +s_9646 CCDC170 0 +s_9710 CCDC40 0 +s_9732 CCDC48 0 +s_976 ADAM21 0 +s_9763 CCDC62 0 +s_9868 CCDC89 0 +s_991 ADAM30 0 +s_9925 CCL1 0 +s_9973 CCL26 0 diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.R --- a/test-data/out.test.R Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.test.R Wed Apr 04 11:03:59 2018 -0400 @@ -10,7 +10,7 @@ # outputfile='__OUTPUT_FILE__' targetgenelist=c("ACIN1","ACTR8","AHCY","ACLY","AATF","AGBL5","AHCTF1","ABT1","ADIRF","ABCF1") # samplelabel=sub('.\\w+.\\w+$','',colnames(gstable)[startindex]); -samplelabel='HL60.final,KBM7.final_vs_HL60.initial,KBM7.initial neg.' +samplelabel='HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial neg.' # You need to write some codes in front of this code: @@ -116,7 +116,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(561.4907165816957,824.0396348113272,428.37415340969943,579.047491896501),c(3424.79939695118,3818.2871009576584,1992.3498917052,690.0506672205338),c(846.6456878299913,985.6508562937211,335.0024675413113,415.97581680707134),c(2432.636481525409,2122.257249136931,1067.465489792653,155.6333179800872),c(1308.1851773762019,2186.1913587343615,1482.5909580453515,997.3120339679854),c(405.68439208520414,268.16807081144486,170.34023773287015,109.85881269182627),c(640.8637498157573,559.4234589775174,711.6436598617687,632.2603542941043),c(946.5969148654764,470.6260845366416,663.0651476194316,457.74505288260946),c(246.9383256170808,177.59474888175154,28.39003962214503,0.0),c(568.8400715107754,612.7018836420428,564.0154538266146,270.64176251684285)) targetgene="ACIN1" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -151,7 +151,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(2484.0819660289676,2349.578527705573,2172.7843657481662,910.9126552363929),c(992.1629154257711,1005.1862786707138,743.8190381001997,200.26346063614164),c(1267.0287897733551,1156.1418152202027,251.09412821363824,42.34141739164138),c(1500.738276518092,1315.977089213779,800.5991173444897,1476.2277955464156),c(1925.5309914189038,2054.7712445618654,194.94493873872918,235.16652091844063),c(351.29916561001374,781.4168950797068,227.75120674654121,624.2498158686586),c(1719.74905340467,1006.9622261595313,356.45271970026533,222.0063506480656),c(903.9706562768137,1445.6212558974576,1482.5909580453515,1055.1023468944147),c(651.152846716469,1081.552020689867,576.0023594448536,1072.2677863775127),c(285.1549712482957,408.46792242802854,99.0496937928171,44.630142656054424)) targetgene="ACTR8" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -186,7 +186,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(301.3235520922712,657.1005708624807,228.38209651592223,137.32351586478285),c(1142.0897559789987,1099.311495578042,112.92926871919911,100.70391163417409),c(789.3207193831689,671.3081507730209,723.6305654800077,588.7745742702564),c(392.45555321286054,412.0198174056636,334.37157777193033,213.99581222261992),c(2009.3136376104133,2235.917888421252,2437.1271791188055,1937.9781176417478),c(1071.5359486598327,406.69197493921104,645.4002340767636,349.602784139093),c(61.7345814042702,218.44154112455442,614.4866353770946,452.5954210376801),c(651.152846716469,879.0940069646701,237.21455328725622,18.88198343140764),c(1625.6773103124485,1410.1023061211074,2146.286995434164,1986.613529510525),c(1053.8974968300413,882.6459019423052,106.6203710253891,105.85354347910344)) targetgene="AHCY" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -221,7 +221,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(1268.498660759171,1411.8782536099247,1136.2324746551822,603.6512884889412),c(327.78122983695846,454.642557137284,51.73296108924205,24.031615276336996),c(132.28838872343613,241.5288584791821,123.02350502929512,65.80085135187511),c(495.34652221997754,586.0626713097802,279.4841678357833,243.74924065998954),c(1009.8013672555626,1102.8633905556771,1237.174837756142,1004.7503910773278),c(877.5129785321263,715.7068379934587,538.1489732819936,594.496387431289),c(1594.8100196103135,1108.1912330221296,605.6541786057605,127.59643349102738),c(314.5523909646148,252.1845434120872,88.95545748272109,359.9020478289517),c(512.984974049769,269.94401830026237,205.67006481820619,126.45207085882086),c(761.3931706526657,475.9539270030942,559.5992254409475,596.7851126957021)) targetgene="ACLY" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -256,7 +256,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(659.9720726313648,809.832054900787,880.7221180558769,802.1982051767731),c(724.6463960072668,1086.8798631563195,695.2405258578626,307.26136674745163),c(836.3565909292796,1289.3378768815162,468.75109865008346,177.94838930811443),c(367.46774645398926,571.85509139924,300.30353022535627,116.72498848506541),c(518.8644579930328,632.2373060190355,627.7353205340956,308.9779106957614),c(405.68439208520414,259.28833336735727,324.27734146183434,166.5047629860492),c(2096.0360257735547,1960.6460276545372,1573.4390848362154,629.9716290296913),c(277.8056163192159,435.1071347602913,182.32714335110919,0.0),c(995.1026573974029,477.7298744919117,728.0467938656747,275.21921304566894),c(2185.6981559083283,1482.9161531626255,1741.8866532609427,1862.4501839161173)) targetgene="AATF" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -291,7 +291,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(640.8637498157573,602.0461987091378,307.2433176885473,192.82510352679924),c(354.23890758164566,280.5997032331675,204.4082852794442,275.79139436177223),c(779.0316224824572,932.3724316291956,778.5179754161547,905.1908420753603),c(624.6951689717818,554.0956165110648,370.96318439602834,558.4489645167836),c(1133.270530064103,1394.1187787217498,639.0913363829536,1131.2024619361487),c(423.32284391499564,412.0198174056636,224.59675789963623,426.84726181303336),c(296.91393913482335,829.3674772777797,489.5704610396565,1233.0507362025292),c(684.959879390236,546.9918265557948,394.30610586312537,566.4595029422292),c(440.96129574478715,630.461358530218,434.6830511035094,457.1728715665062),c(1108.2827233052317,1969.5257650986248,1066.2037102538911,1333.7546478367033)) targetgene="AGBL5" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -326,7 +326,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(196.96271209933826,301.9110730989776,423.9579250240324,34.33087896619571),c(1106.8128523194157,1056.6887558464218,1743.1484327997048,807.3478370217025),c(748.1643317803222,488.3855594248168,239.73811236478022,477.77139894622366),c(1095.053884432888,882.6459019423052,837.8216137379688,365.05167967388104),c(677.6105244611563,316.11865300951774,613.8557456077136,819.3636446598709),c(1078.8853035889126,1609.008424868669,348.88204246769334,193.96946615900578),c(1437.533824128006,1095.759600600407,320.4920028455483,161.35513114111984),c(845.1758168441753,660.6524658401157,541.3034221288985,640.8430740356532),c(551.2016196809839,740.570102836904,1103.42620664737,622.5332719203489),c(601.1772331987264,900.4053768304803,735.6174710982467,754.1349746240991)) targetgene="AHCTF1" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -361,7 +361,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(487.9971672908978,367.6211301852257,312.2904358435953,441.15179471561487),c(358.6485205390935,394.2603425174884,593.0363832181406,268.35303725242983),c(1743.266989177725,1980.1814500315297,837.1907239685878,281.5132075228048),c(1597.7497615819454,1465.1566782744503,1065.57282048451,992.7345834391593),c(119.05954985109253,378.2768151181308,185.48159219801417,128.7407961232339),c(986.2834314825072,745.8979453033566,328.0626800781203,302.11173490252224),c(523.2740709504807,694.3954681276485,336.89513684945433,597.9294753279087),c(1562.4728579223624,763.6574201915316,422.0652557158894,220.28980669975581),c(30.8672907021351,179.37069637056908,238.47633282601822,184.81456510135357),c(339.5401977234861,447.5387671820139,310.3977665354523,205.98527379717427)) targetgene="ABT1" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -396,7 +396,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(492.4067802483456,221.99343610218943,309.7668767660713,102.99263689858714),c(243.9985836454489,239.7529109903646,130.59418226186713,174.51530141149487),c(734.9354929079785,673.0840982618383,620.7955330709046,470.9052231529845),c(1074.4756906314647,950.1319065173708,1100.902647569846,743.8357109342404),c(702.5983312200275,1010.5141211371663,1291.4313579229083,1017.3383800315995),c(1647.7253750996879,760.1055252138966,685.7771793171477,608.2287390177673),c(951.0065278229242,864.8864270541301,606.9159581445226,769.0116888427839),c(435.0818118015233,435.1071347602913,275.69882921949727,339.8757017653375),c(89.66213013477338,209.56180368046682,208.8245136651112,304.4004601669353),c(1328.7633711776252,1571.7135276035012,1122.983789498181,1356.6419004808338)) targetgene="ADIRF" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -431,7 +431,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(216.0710349149457,289.479440677255,192.42137966120518,498.36992632594104),c(1127.391046120839,1198.764554951823,371.5940741654094,370.2013115188104),c(1111.2224652768637,1038.9292809582466,948.227323379644,922.3562815584581),c(1164.137820766238,1204.0923974182756,1686.9992433247955,2089.033985093009),c(48.505742531926586,248.63264843445216,665.5887066969557,248.8988725049189),c(501.2260061632414,387.1565525622184,436.5757204116524,314.69972385679404),c(1975.5066049366465,1797.2588586833258,1628.3264947723626,1289.6966864967521),c(213.13129294331378,376.5008676293133,404.4003421732214,482.921030791153),c(2012.2533795820452,1989.0611874756173,1064.3110409457481,431.9968936579627),c(264.57677744687226,353.4135502746856,442.25372833608145,191.6807408945927)) targetgene="ABCF1" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -471,7 +471,7 @@ # outputfile='__OUTPUT_FILE__' targetgenelist=c("ACRC","AGAP3","ADCK4","AHRR","ADRBK1","ADK","ADCK1","ADARB2","ACSS2","ADNP") # samplelabel=sub('.\\w+.\\w+$','',colnames(gstable)[startindex]); -samplelabel='HL60.final,KBM7.final_vs_HL60.initial,KBM7.initial pos.' +samplelabel='HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial pos.' # You need to write some codes in front of this code: @@ -577,7 +577,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(461.5394895462105,502.5931393353569,445.40817718298644,889.1697652244688),c(76.43329126242978,90.5733219296933,447.30084649112945,357.0411412484354),c(258.6972935036084,685.515730683561,533.7327448963265,560.7376897811967),c(232.23961575892122,681.9638357059259,275.69882921949727,467.47213525636494),c(1393.4376945535273,1472.2604682297203,1039.706339939889,532.7008052921368),c(2395.88970688001,2441.927797124084,2462.9936596634266,2461.5240218762324),c(495.34652221997754,605.5980936867728,1159.575396122279,1617.5565806239213),c(682.0201374186041,822.2636873225097,1572.1773052974536,1333.7546478367033),c(961.2956247236359,1097.5355480892247,959.5833392285019,905.1908420753603),c(1940.2297012770634,1289.3378768815162,942.5493154552149,1103.737758763192)) targetgene="ACRC" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -612,7 +612,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(1387.5582106102636,1120.6228654438523,1214.4628060584262,1111.1761158725344),c(388.0459402554127,509.69692929062694,933.0859689144999,750.1297054113762),c(326.3113588511425,635.7892009966705,960.8451187672639,615.6670961271097),c(1328.7633711776252,1038.9292809582466,1346.3187678590552,1596.3858719281006),c(352.7690365958297,234.42506852391205,310.3977665354523,429.1359870774464),c(693.7791053051318,678.4119407282909,784.1959833405838,895.4637597016048),c(837.8264619150956,719.2587329710938,374.74852301231437,993.8789460713658),c(365.99787546817333,369.3970776740432,333.74068800254935,746.6966175147567),c(707.0079441774753,635.7892009966705,837.1907239685878,1465.3563505404536),c(486.5272963050818,673.0840982618383,784.8268731099647,734.6808098765882)) targetgene="AGAP3" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -647,7 +647,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(830.4771069860158,864.8864270541301,1349.4732167059603,740.974804353724),c(1481.6299537024847,1994.38902994207,2044.082852794442,1810.9538654668238),c(1234.6916280854039,1299.9935618144214,1357.6747837079133,2232.6514954349277),c(224.89026082984142,188.25043381465665,700.2876440129107,81.24974688666317),c(812.8386551562243,845.3510046771374,946.334654071501,999.6007592323984),c(1978.4463469082782,1751.0842239740703,2659.2003779409174,2851.1794981425537),c(565.9003295391435,776.0890526132542,878.1985589783528,445.72924524444096),c(680.5502664327881,534.5601941340722,550.7667686696135,1025.9210997731484),c(161.68580843975528,333.87812789769293,275.0679394501163,465.18340999195186),c(2523.768482645998,2445.4796921017187,2153.226782897355,1516.8526689897471)) targetgene="ADCK4" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -682,7 +682,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(345.4196816667499,163.38716897121142,474.42910657451245,481.2044868428432),c(415.9734889859159,372.9489726516783,212.6098522813972,349.03060282298975),c(1.469870985815957,83.46953197442323,0.0,62.9399447713588),c(351.29916561001374,150.9555365494888,288.9475143764983,416.54799812317464),c(561.4907165816957,170.49095892648148,199.3611671243962,411.97054759434855),c(251.34793857452865,221.99343610218943,1564.6066280648815,1502.5481360871656),c(736.4053638937945,893.3015868752103,1114.782222496228,459.46159683091923),c(338.07032673767014,607.3740411755903,378.5338616286004,65.22867003577186),c(1230.2820151279561,525.6804566899846,837.1907239685878,945.2435342025885)) targetgene="AHRR" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -717,7 +717,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(371.87735941143717,877.3180594758527,2395.4884543396593,1564.9158995424211),c(1109.7525942910477,1138.3823403320275,970.308465307979,999.0285779162951),c(1462.5216308868773,1209.420239884728,1537.4783679814984,1519.14139425416),c(586.4785233405669,987.4268037825386,743.8190381001997,1312.0117578247794),c(1018.6205931704583,717.4827854822763,1070.619938639558,1144.3626322065236),c(1269.9685317449869,1212.9721348623632,1591.1039983788835,1624.9949377332637),c(1321.4140162485455,1795.4829111945082,1478.8056194290655,1237.056005415252),c(908.3802692342615,832.9193722554148,1639.6825106212207,1268.5259778009315),c(923.078979092421,758.3295777250792,1479.4365091984464,1275.964334910274),c(680.5502664327881,634.013253507853,318.5993335374053,631.1159916618979)) targetgene="ADRBK1" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -752,7 +752,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(1472.810727787589,1829.225913482041,1263.0413183007631,1315.444845721399),c(208.7216799858659,65.71005708624807,292.1019632234033,350.17496545519623),c(1011.2712382413785,1166.7975001531076,652.9709113093356,860.5606994193058),c(557.0811036242477,685.515730683561,875.0441101314478,1019.6271052960126),c(363.0581334965414,825.8155823001447,736.8792506370087,349.602784139093),c(1505.14788947554,451.09066215964896,653.6018010787167,991.0180394908496),c(198.43258308515422,28.41515982108025,249.83234867487624,114.43626322065236),c(438.02155377315523,74.58979453033565,254.87946682992424,231.16125170571777),c(804.0194292413286,472.4020320254591,1336.2245315489592,1203.2973077651598),c(454.19013461713075,490.1615069136343,896.4943622904019,685.4732166917076)) targetgene="ADK" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -787,7 +787,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(662.9118146029966,1008.7381736483488,1101.533537339227,1694.8010582978616),c(1547.7741480642028,1965.9738701209897,1869.9572764452857,2353.9539344488194),c(1459.5818889152454,1179.2291325748304,1296.4784760779562,1222.1792911965672),c(1193.5352404825571,1355.0479339677643,1622.0175970785526,1905.9359639399652),c(868.6937526172306,701.4992580829187,720.4761166331027,603.6512884889412),c(798.1399452980647,768.9852626579842,1478.8056194290655,1756.0244591209105),c(1168.5474337236858,907.5091667857504,879.4603385171149,977.8578692204745),c(809.8989131845924,687.2916781723785,678.8373918539567,865.7103312642352),c(1246.4505959719315,753.0017352586266,1301.5255942330043,1264.5207085882087),c(826.0674940285679,797.4004224790644,977.8791425405509,2066.7189137649816)) targetgene="ADCK1" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -822,7 +822,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(1863.7964100146337,1585.9211075140413,1761.4442361117538,1464.211987908247),c(742.2848478370584,598.4943037315028,943.8110949939769,820.5080072920774),c(1568.3523418656262,2083.1864043829455,1810.6536381234716,1887.6261618246608),c(1018.6205931704583,513.248824268262,679.4682816233377,824.5132765048003),c(1140.6198849931827,1191.6607649965529,880.0912282864958,977.8578692204745),c(135.22813069506805,118.98848175077354,351.40560154521734,399.95473995618005),c(665.8515565746286,701.4992580829187,986.7115993118849,746.6966175147567),c(418.9132309575478,300.1351256101601,376.6411923204574,645.4205245644794),c(561.4907165816957,543.4399315781598,881.9838975946388,580.7640358448108),c(442.4311667306031,229.0972260574595,395.5678854018874,651.142337725512)) targetgene="ADARB2" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -857,7 +857,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(734.9354929079785,358.74139274113816,541.9343118982795,378.7840312603593),c(595.2977492554626,591.3905137762326,1061.787481868224,887.4532212761591),c(1655.0747300287676,943.0281165621008,1069.358159100796,2038.1098479598186),c(626.1650399575977,884.4218494311227,517.3296108924205,858.2719741548927),c(680.5502664327881,747.673892792174,533.1018551269456,1016.194017399393),c(662.9118146029966,777.8650001020718,864.9498738213518,787.3214909580882),c(880.4527205037583,621.5816210861304,671.8976043907657,1040.7978139918332),c(94.07174309222125,447.5387671820139,711.6436598617687,927.5059134033875),c(399.80490814194036,806.280159923152,1147.58849050404,1059.1076161071376),c(698.1887182625796,531.0082991564371,504.0809257354195,347.8862401907832)) targetgene="ACSS2" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) @@ -892,7 +892,7 @@ # Do not modify the variables beginning with "__" targetmat=list(c(408.62413405683606,523.9045092011671,483.89245311522745,701.494293542599),c(1805.0015705819953,1434.9655709645526,1712.2348341000356,2152.546111180471),c(3017.64513388016,2642.609863360463,1834.6274493599499,3573.2723190648703),c(1649.1952460855039,783.1928425685244,773.4708572611067,1332.0381038883936),c(959.82575373782,1397.6706736993847,1429.5962174173474,2811.126806015325),c(495.34652221997754,301.9110730989776,336.89513684945433,555.015876620164),c(1491.9190506031964,1331.9606166131366,2087.614246881731,1983.1804416139055),c(429.2023278582595,889.7496918975753,567.8007924429005,1132.9190058844583),c(427.7324568724435,573.6310388880576,655.4944703868597,899.4690289143276),c(690.8393633334998,767.2093151691668,1040.33722970927,993.3067647552625)) targetgene="ADNP" -collabel=c("HL60.initial","KBM7.initial","HL60.final","KBM7.final") +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") # set up color using RColorBrewer #library(RColorBrewer) diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.log.txt --- a/test-data/out.test.log.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.test.log.txt Wed Apr 04 11:03:59 2018 -0400 @@ -1,112 +1,109 @@ -INFO @ Mon, 12 Feb 2018 03:40:01: Parameters: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/bin/mageck test -k /tmp/tmp0xS0Jl/files/000/dataset_21.dat -t HL60.final,KBM7.final -c HL60.initial,KBM7.initial -n output --normcounts-to-file --pdf-report --norm-method median --gene-test-fdr-threshold 0.25 --adjust-method fdr --sort-criteria neg --remove-zero none --gene-lfc-method median -INFO @ Mon, 12 Feb 2018 03:40:01: Welcome to MAGeCK v0.5.7. Command: test -INFO @ Mon, 12 Feb 2018 03:40:01: Loading count table from /tmp/tmp0xS0Jl/files/000/dataset_21.dat -INFO @ Mon, 12 Feb 2018 03:40:01: Processing 1 lines.. -DEBUG @ Mon, 12 Feb 2018 03:40:01: Parsing error in line 1 (usually the header line). Skip this line. -INFO @ Mon, 12 Feb 2018 03:40:01: Loaded 999 records. -INFO @ Mon, 12 Feb 2018 03:40:01: Loading R template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template.RTemplate. -INFO @ Mon, 12 Feb 2018 03:40:01: Loading R template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template_indvgene.RTemplate. -INFO @ Mon, 12 Feb 2018 03:40:01: Loading Rnw template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template.Rnw. -DEBUG @ Mon, 12 Feb 2018 03:40:01: Setting up the visualization module... -DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.final,KBM7.final -DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 2 3 -INFO @ Mon, 12 Feb 2018 03:40:01: Treatment samples:HL60.final,KBM7.final -INFO @ Mon, 12 Feb 2018 03:40:01: Treatment sample index:2,3 -DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.initial,KBM7.initial -DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 0 1 -INFO @ Mon, 12 Feb 2018 03:40:01: Control samples:HL60.initial,KBM7.initial -INFO @ Mon, 12 Feb 2018 03:40:01: Control sample index:0,1 -DEBUG @ Mon, 12 Feb 2018 03:40:01: Initial (total) size factor: 1.6666455325878438 2.027372749328462 0.7198064117880387 0.6589869375844738 -DEBUG @ Mon, 12 Feb 2018 03:40:01: Median factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 -INFO @ Mon, 12 Feb 2018 03:40:01: Final size factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 -INFO @ Mon, 12 Feb 2018 03:40:01: Writing normalized read counts to output.normalized.txt -DEBUG @ Mon, 12 Feb 2018 03:40:01: Adjusted model: 1.1175084644498339 3.4299551007579927 -INFO @ Mon, 12 Feb 2018 03:40:01: Raw variance calculation: 0.5 for control, 0.5 for treatment -INFO @ Mon, 12 Feb 2018 03:40:01: Adjusted variance calculation: 0.3333333333333333 for raw variance, 0.6666666666666667 for modeling -INFO @ Mon, 12 Feb 2018 03:40:01: Use qnorm to reversely calculate sgRNA scores ... -DEBUG @ Mon, 12 Feb 2018 03:40:01: lower test FDR cutoff: 0.3283283283283283 -DEBUG @ Mon, 12 Feb 2018 03:40:01: higher test FDR cutoff: 0.34534534534534533 -INFO @ Mon, 12 Feb 2018 03:40:01: Running command: RRA -i output.plow.txt -o output.gene.low.txt -p 0.3283283283283283 --skip-gene NA --skip-gene na -INFO @ Mon, 12 Feb 2018 03:40:02: Command message: -INFO @ Mon, 12 Feb 2018 03:40:02: Welcome to RRA v 0.5.7. -INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene NA for permutation ... -INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene na for permutation ... -INFO @ Mon, 12 Feb 2018 03:40:02: Reading input file... -INFO @ Mon, 12 Feb 2018 03:40:02: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 -INFO @ Mon, 12 Feb 2018 03:40:02: Computing lo-values for each group... -INFO @ Mon, 12 Feb 2018 03:40:02: Computing false discovery rate... -INFO @ Mon, 12 Feb 2018 03:40:02: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option. -INFO @ Mon, 12 Feb 2018 03:40:02: Permuting genes with 9 sgRNAs... -INFO @ Mon, 12 Feb 2018 03:40:02: Permuting genes with 10 sgRNAs... -INFO @ Mon, 12 Feb 2018 03:40:02: Number of genes under FDR adjustment: 100 -INFO @ Mon, 12 Feb 2018 03:40:02: Saving to output file... -INFO @ Mon, 12 Feb 2018 03:40:02: RRA completed. -INFO @ Mon, 12 Feb 2018 03:40:02: -INFO @ Mon, 12 Feb 2018 03:40:02: End command message. -INFO @ Mon, 12 Feb 2018 03:40:02: Running command: RRA -i output.phigh.txt -o output.gene.high.txt -p 0.34534534534534533 --skip-gene NA --skip-gene na -INFO @ Mon, 12 Feb 2018 03:40:03: Command message: -INFO @ Mon, 12 Feb 2018 03:40:03: Welcome to RRA v 0.5.7. -INFO @ Mon, 12 Feb 2018 03:40:03: Skipping gene NA for permutation ... -INFO @ Mon, 12 Feb 2018 03:40:03: Skipping gene na for permutation ... -INFO @ Mon, 12 Feb 2018 03:40:03: Reading input file... -INFO @ Mon, 12 Feb 2018 03:40:03: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 -INFO @ Mon, 12 Feb 2018 03:40:03: Computing lo-values for each group... -INFO @ Mon, 12 Feb 2018 03:40:03: Computing false discovery rate... -INFO @ Mon, 12 Feb 2018 03:40:03: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option. -INFO @ Mon, 12 Feb 2018 03:40:03: Permuting genes with 9 sgRNAs... -INFO @ Mon, 12 Feb 2018 03:40:03: Permuting genes with 10 sgRNAs... -INFO @ Mon, 12 Feb 2018 03:40:03: Number of genes under FDR adjustment: 100 -INFO @ Mon, 12 Feb 2018 03:40:03: Saving to output file... -INFO @ Mon, 12 Feb 2018 03:40:03: RRA completed. -INFO @ Mon, 12 Feb 2018 03:40:03: -INFO @ Mon, 12 Feb 2018 03:40:03: End command message. -DEBUG @ Mon, 12 Feb 2018 03:40:03: Sorting the merged items by negative selection... -INFO @ Mon, 12 Feb 2018 03:40:03: Loading top 10 genes from output.gene.low.txt: ACIN1,ACTR8,AHCY,ACLY,AATF,AGBL5,AHCTF1,ABT1,ADIRF,ABCF1 -DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:3 -INFO @ Mon, 12 Feb 2018 03:40:03: Loading top 10 genes from output.gene.high.txt: ACRC,AGAP3,ADCK4,AHRR,ADRBK1,ADK,ADCK1,ADARB2,ACSS2,ADNP -DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:9 -INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.plow.txt -INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.phigh.txt -INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.low.txt -INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.high.txt -INFO @ Mon, 12 Feb 2018 03:40:03: Running command: cd ./; Rscript output.R -INFO @ Mon, 12 Feb 2018 03:40:04: Command message: -INFO @ Mon, 12 Feb 2018 03:40:04: null device -INFO @ Mon, 12 Feb 2018 03:40:04: 1 -INFO @ Mon, 12 Feb 2018 03:40:04: Writing to file output_summary.tex -INFO @ Mon, 12 Feb 2018 03:40:04: Processing code chunks with options ... -INFO @ Mon, 12 Feb 2018 03:40:04: 1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27) -INFO @ Mon, 12 Feb 2018 03:40:04: 2 : keep.source term tex (label = tab1, output_summary.Rnw:37) -INFO @ Mon, 12 Feb 2018 03:40:04: 3 : keep.source term verbatim (output_summary.Rnw:77) -INFO @ Mon, 12 Feb 2018 03:40:04: 4 : keep.source term verbatim pdf (output_summary.Rnw:83) -INFO @ Mon, 12 Feb 2018 03:40:04: 5 : keep.source term verbatim pdf (output_summary.Rnw:201) -INFO @ Mon, 12 Feb 2018 03:40:04: 6 : keep.source term verbatim pdf (output_summary.Rnw:345) -INFO @ Mon, 12 Feb 2018 03:40:04: 7 : keep.source term verbatim pdf (output_summary.Rnw:489) -INFO @ Mon, 12 Feb 2018 03:40:04: 8 : keep.source term verbatim (output_summary.Rnw:567) -INFO @ Mon, 12 Feb 2018 03:40:04: 9 : keep.source term verbatim pdf (output_summary.Rnw:573) -INFO @ Mon, 12 Feb 2018 03:40:04: 10 : keep.source term verbatim pdf (output_summary.Rnw:691) -INFO @ Mon, 12 Feb 2018 03:40:04: 11 : keep.source term verbatim pdf (output_summary.Rnw:835) -INFO @ Mon, 12 Feb 2018 03:40:04: 12 : keep.source term verbatim pdf (output_summary.Rnw:979) -INFO @ Mon, 12 Feb 2018 03:40:04: -INFO @ Mon, 12 Feb 2018 03:40:04: You can now run (pdf)latex on ‘output_summary.tex’ -INFO @ Mon, 12 Feb 2018 03:40:04: Error in texi2dvi("output_summary.tex", pdf = TRUE) : -INFO @ Mon, 12 Feb 2018 03:40:04: pdflatex is not available -INFO @ Mon, 12 Feb 2018 03:40:04: Execution halted -INFO @ Mon, 12 Feb 2018 03:40:04: -INFO @ Mon, 12 Feb 2018 03:40:04: End command message. -INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary-*.pdf -INFO @ Mon, 12 Feb 2018 03:40:04: Command message: -INFO @ Mon, 12 Feb 2018 03:40:04: -INFO @ Mon, 12 Feb 2018 03:40:04: End command message. -INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.aux -INFO @ Mon, 12 Feb 2018 03:40:04: Command message: -INFO @ Mon, 12 Feb 2018 03:40:04: -INFO @ Mon, 12 Feb 2018 03:40:04: End command message. -INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.tex -INFO @ Mon, 12 Feb 2018 03:40:04: Command message: -INFO @ Mon, 12 Feb 2018 03:40:04: -INFO @ Mon, 12 Feb 2018 03:40:04: End command message. -INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.toc -INFO @ Mon, 12 Feb 2018 03:40:04: Command message: -INFO @ Mon, 12 Feb 2018 03:40:04: -INFO @ Mon, 12 Feb 2018 03:40:04: End command message. +INFO @ Mon, 26 Mar 2018 08:37:53: Parameters: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/bin/mageck test -k /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpTX65kA/files/000/dataset_4.dat -t HL60_final,KBM7_final -c HL60_initial,KBM7_initial -n output --normcounts-to-file --pdf-report --norm-method median --adjust-method fdr --sort-criteria neg --remove-zero both --gene-lfc-method median +INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to MAGeCK v0.5.7. Command: test +INFO @ Mon, 26 Mar 2018 08:37:53: Loading count table from /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpTX65kA/files/000/dataset_4.dat +INFO @ Mon, 26 Mar 2018 08:37:53: Processing 1 lines.. +DEBUG @ Mon, 26 Mar 2018 08:37:53: Parsing error in line 1 (usually the header line). Skip this line. +INFO @ Mon, 26 Mar 2018 08:37:53: Loaded 999 records. +INFO @ Mon, 26 Mar 2018 08:37:53: Loading R template file: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/lib/python3.6/site-packages/mageck/plot_template.RTemplate. +INFO @ Mon, 26 Mar 2018 08:37:53: Loading R template file: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/lib/python3.6/site-packages/mageck/plot_template_indvgene.RTemplate. +INFO @ Mon, 26 Mar 2018 08:37:53: Loading Rnw template file: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/lib/python3.6/site-packages/mageck/plot_template.Rnw. +DEBUG @ Mon, 26 Mar 2018 08:37:53: Setting up the visualization module... +DEBUG @ Mon, 26 Mar 2018 08:37:53: Given sample labels: HL60_final,KBM7_final +DEBUG @ Mon, 26 Mar 2018 08:37:53: Converted index: 2 3 +INFO @ Mon, 26 Mar 2018 08:37:53: Treatment samples:HL60_final,KBM7_final +INFO @ Mon, 26 Mar 2018 08:37:53: Treatment sample index:2,3 +DEBUG @ Mon, 26 Mar 2018 08:37:53: Given sample labels: HL60_initial,KBM7_initial +DEBUG @ Mon, 26 Mar 2018 08:37:53: Converted index: 0 1 +INFO @ Mon, 26 Mar 2018 08:37:53: Control samples:HL60_initial,KBM7_initial +INFO @ Mon, 26 Mar 2018 08:37:53: Control sample index:0,1 +DEBUG @ Mon, 26 Mar 2018 08:37:53: Initial (total) size factor: 1.6666455325878438 2.027372749328462 0.7198064117880387 0.6589869375844738 +DEBUG @ Mon, 26 Mar 2018 08:37:53: Median factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 +INFO @ Mon, 26 Mar 2018 08:37:53: Final size factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 +INFO @ Mon, 26 Mar 2018 08:37:53: Writing normalized read counts to output.normalized.txt +DEBUG @ Mon, 26 Mar 2018 08:37:53: Adjusted model: 1.1175084644498339 3.4299551007579927 +INFO @ Mon, 26 Mar 2018 08:37:53: Raw variance calculation: 0.5 for control, 0.5 for treatment +INFO @ Mon, 26 Mar 2018 08:37:53: Adjusted variance calculation: 0.3333333333333333 for raw variance, 0.6666666666666667 for modeling +INFO @ Mon, 26 Mar 2018 08:37:53: Use qnorm to reversely calculate sgRNA scores ... +DEBUG @ Mon, 26 Mar 2018 08:37:53: lower test FDR cutoff: 0.3283283283283283 +DEBUG @ Mon, 26 Mar 2018 08:37:53: higher test FDR cutoff: 0.34534534534534533 +INFO @ Mon, 26 Mar 2018 08:37:53: Running command: RRA -i output.plow.txt -o output.gene.low.txt -p 0.3283283283283283 --skip-gene NA --skip-gene na +INFO @ Mon, 26 Mar 2018 08:37:53: Command message: +INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to RRA v 0.5.7. +INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene NA for permutation ... +INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene na for permutation ... +INFO @ Mon, 26 Mar 2018 08:37:53: Reading input file... +INFO @ Mon, 26 Mar 2018 08:37:53: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 +INFO @ Mon, 26 Mar 2018 08:37:53: Computing lo-values for each group... +INFO @ Mon, 26 Mar 2018 08:37:53: Computing false discovery rate... +INFO @ Mon, 26 Mar 2018 08:37:53: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option. +INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 9 sgRNAs... +INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 10 sgRNAs... +INFO @ Mon, 26 Mar 2018 08:37:53: Number of genes under FDR adjustment: 100 +INFO @ Mon, 26 Mar 2018 08:37:53: Saving to output file... +INFO @ Mon, 26 Mar 2018 08:37:53: RRA completed. +INFO @ Mon, 26 Mar 2018 08:37:53: +INFO @ Mon, 26 Mar 2018 08:37:53: End command message. +INFO @ Mon, 26 Mar 2018 08:37:53: Running command: RRA -i output.phigh.txt -o output.gene.high.txt -p 0.34534534534534533 --skip-gene NA --skip-gene na +INFO @ Mon, 26 Mar 2018 08:37:53: Command message: +INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to RRA v 0.5.7. +INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene NA for permutation ... +INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene na for permutation ... +INFO @ Mon, 26 Mar 2018 08:37:53: Reading input file... +INFO @ Mon, 26 Mar 2018 08:37:53: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 +INFO @ Mon, 26 Mar 2018 08:37:53: Computing lo-values for each group... +INFO @ Mon, 26 Mar 2018 08:37:53: Computing false discovery rate... +INFO @ Mon, 26 Mar 2018 08:37:53: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option. +INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 9 sgRNAs... +INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 10 sgRNAs... +INFO @ Mon, 26 Mar 2018 08:37:53: Number of genes under FDR adjustment: 100 +INFO @ Mon, 26 Mar 2018 08:37:53: Saving to output file... +INFO @ Mon, 26 Mar 2018 08:37:53: RRA completed. +INFO @ Mon, 26 Mar 2018 08:37:53: +INFO @ Mon, 26 Mar 2018 08:37:53: End command message. +DEBUG @ Mon, 26 Mar 2018 08:37:53: Sorting the merged items by negative selection... +INFO @ Mon, 26 Mar 2018 08:37:53: Loading top 10 genes from output.gene.low.txt: ACIN1,ACTR8,AHCY,ACLY,AATF,AGBL5,AHCTF1,ABT1,ADIRF,ABCF1 +DEBUG @ Mon, 26 Mar 2018 08:37:53: Column index:3 +INFO @ Mon, 26 Mar 2018 08:37:53: Loading top 10 genes from output.gene.high.txt: ACRC,AGAP3,ADCK4,AHRR,ADRBK1,ADK,ADCK1,ADARB2,ACSS2,ADNP +DEBUG @ Mon, 26 Mar 2018 08:37:53: Column index:9 +INFO @ Mon, 26 Mar 2018 08:37:53: Running command: rm output.plow.txt +INFO @ Mon, 26 Mar 2018 08:37:53: Running command: rm output.phigh.txt +INFO @ Mon, 26 Mar 2018 08:37:54: Running command: rm output.gene.low.txt +INFO @ Mon, 26 Mar 2018 08:37:54: Running command: rm output.gene.high.txt +INFO @ Mon, 26 Mar 2018 08:37:54: Running command: cd ./; Rscript output.R +INFO @ Mon, 26 Mar 2018 08:37:59: Command message: +INFO @ Mon, 26 Mar 2018 08:37:59: null device +INFO @ Mon, 26 Mar 2018 08:37:59: 1 +INFO @ Mon, 26 Mar 2018 08:37:59: Writing to file output_summary.tex +INFO @ Mon, 26 Mar 2018 08:37:59: Processing code chunks with options ... +INFO @ Mon, 26 Mar 2018 08:37:59: 1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27) +INFO @ Mon, 26 Mar 2018 08:37:59: 2 : keep.source term tex (label = tab1, output_summary.Rnw:37) +INFO @ Mon, 26 Mar 2018 08:37:59: 3 : keep.source term verbatim (output_summary.Rnw:77) +INFO @ Mon, 26 Mar 2018 08:37:59: 4 : keep.source term verbatim pdf (output_summary.Rnw:83) +INFO @ Mon, 26 Mar 2018 08:37:59: 5 : keep.source term verbatim pdf (output_summary.Rnw:201) +INFO @ Mon, 26 Mar 2018 08:37:59: 6 : keep.source term verbatim pdf (output_summary.Rnw:345) +INFO @ Mon, 26 Mar 2018 08:37:59: 7 : keep.source term verbatim pdf (output_summary.Rnw:489) +INFO @ Mon, 26 Mar 2018 08:37:59: 8 : keep.source term verbatim (output_summary.Rnw:567) +INFO @ Mon, 26 Mar 2018 08:37:59: 9 : keep.source term verbatim pdf (output_summary.Rnw:573) +INFO @ Mon, 26 Mar 2018 08:37:59: 10 : keep.source term verbatim pdf (output_summary.Rnw:691) +INFO @ Mon, 26 Mar 2018 08:37:59: 11 : keep.source term verbatim pdf (output_summary.Rnw:835) +INFO @ Mon, 26 Mar 2018 08:37:59: 12 : keep.source term verbatim pdf (output_summary.Rnw:979) +INFO @ Mon, 26 Mar 2018 08:37:59: +INFO @ Mon, 26 Mar 2018 08:37:59: You can now run (pdf)latex on ‘output_summary.tex’ +INFO @ Mon, 26 Mar 2018 08:37:59: +INFO @ Mon, 26 Mar 2018 08:37:59: End command message. +INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary-*.pdf +INFO @ Mon, 26 Mar 2018 08:37:59: Command message: +INFO @ Mon, 26 Mar 2018 08:37:59: +INFO @ Mon, 26 Mar 2018 08:37:59: End command message. +INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.aux +INFO @ Mon, 26 Mar 2018 08:37:59: Command message: +INFO @ Mon, 26 Mar 2018 08:37:59: +INFO @ Mon, 26 Mar 2018 08:37:59: End command message. +INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.tex +INFO @ Mon, 26 Mar 2018 08:37:59: Command message: +INFO @ Mon, 26 Mar 2018 08:37:59: +INFO @ Mon, 26 Mar 2018 08:37:59: End command message. +INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.toc +INFO @ Mon, 26 Mar 2018 08:37:59: Command message: +INFO @ Mon, 26 Mar 2018 08:37:59: +INFO @ Mon, 26 Mar 2018 08:37:59: End command message. diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.normalized.txt --- a/test-data/out.test.normalized.txt Sat Feb 17 10:41:53 2018 -0500 +++ b/test-data/out.test.normalized.txt Wed Apr 04 11:03:59 2018 -0400 @@ -1,4 +1,4 @@ -sgRNA Gene HL60.initial KBM7.initial HL60.final KBM7.final +sgRNA Gene HL60_initial KBM7_initial HL60_final KBM7_final A1CF_m52595977 A1CF 313.08251997879887 486.6096119359992 557.0756663634236 100.13173031807082 A1CF_m52596017 A1CF 432.1420698298914 731.6903653928164 980.402701618075 1081.994868751268 A1CF_m52596056 A1CF 618.8156850285179 653.5486758848457 357.0836094696463 434.28561892237576 diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.pdf Binary file test-data/out.test.pdf has changed diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.plots.pdf Binary file test-data/out.test.plots.pdf has changed diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/out.test.report.pdf Binary file test-data/out.test.report.pdf has changed diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/output.count_normalized.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.count_normalized.txt Wed Apr 04 11:03:59 2018 -0400 @@ -0,0 +1,2551 @@ +sgRNA Gene test1_fastq_gz +s_47512 RNF111 2.0 +s_24835 HCFC1R1 2.0 +s_14784 CYP4B1 8.0 +s_51146 SLC18A1 2.0 +s_58960 TRIM5 2.0 +s_48256 RPRD2 2.0 +s_30297 KRTAP5-5 2.0 +s_14555 CYB5B 2.0 +s_39959 PAAF1 2.0 +s_45293 PUF60 2.0 +s_49358 SCN8A 2.0 +s_64995 ZYG11A 2.0 +s_4029 ASTE1 2.0 +s_45554 R3HDML 2.0 +s_34264 MMRN1 2.0 +s_37459 NOL6 2.0 +s_23990 GPX7 2.0 +s_20268 FANCC 2.0 +s_14157 CTLA4 2.0 +s_36773 NEURL4 36.0 +s_18804 ETFB 2.0 +s_782 ACSS1 2.0 +s_18272 ENPP2 2.0 +s_46620 RCN1 2.0 +s_55436 TAS2R3 2.0 +s_57947 TMPRSS2 2.0 +s_6438 C14orf159 2.0 +s_33846 MGST2 2.0 +s_16328 DNAH6 2.0 +s_17875 EIF4G1 2.0 +s_2305 ANAPC11 2.0 +s_2500 ANKRD2 2.0 +s_82 AARSD1 2.0 +s_55329 TAL1 2.0 +s_57926 TMPRSS11E 16.0 +s_38414 NUP98 8.0 +s_50044 SERPINF1 2.0 +s_9257 CASR 2.0 +s_63396 ZNF182 2.0 +s_56478 THBS3 2.0 +s_17191 DYRK1A 2.0 +s_11988 CIR1 2.0 +s_43313 PPARD 2.0 +s_44681 PSMA4 2.0 +s_10387 CD320 2.0 +s_64869 ZPBP 2.0 +s_54385 STK17B 2.0 +s_25423 HIST1H4D 2.0 +s_54172 ST8SIA4 18.0 +s_1161 ADCY10 2.0 +s_29184 KIAA0913 2.0 +s_42977 POLD3 2.0 +s_49449 SCUBE1 2.0 +s_24181 GRM4 2.0 +s_52507 SMARCA5 2.0 +s_28674 KCNJ10 2.0 +s_61074 VAMP2 8.0 +s_3954 ASIC2 2.0 +s_2385 ANK1 2.0 +s_18397 EPDR1 2.0 +s_18377 EPB41L4B 2.0 +s_34580 MRAP2 2.0 +s_48676 RUFY3 20.0 +s_691 ACP1 2.0 +s_30460 LAMP2 2.0 +s_42637 PLRG1 2.0 +s_12695 CNOT6 2.0 +s_33316 MECOM 4.0 +s_35081 MSRB2 2.0 +s_58512 TPD52L2 2.0 +s_19912 FAM22F 2.0 +s_45517 QSOX2 2.0 +s_56705 TINAG 2.0 +s_10946 CDKL5 2.0 +s_57473 TMEM211 4.0 +s_57657 TMEM44 2.0 +s_43200 POT1 2.0 +s_19436 FAM135A 2.0 +s_184 ABCB9 2.0 +s_30171 KRT84 2.0 +s_44758 PSMC3IP 2.0 +s_48313 RPS3 2.0 +s_58142 TNFSF12 12.0 +s_59718 TTLL6 14.0 +s_9725 CCDC43 2.0 +s_5135 BCKDHA 2.0 +s_36539 NDUFC2 2.0 +s_27251 IL27RA 2.0 +s_48939 SAMD10 2.0 +s_27343 IL5RA 2.0 +s_28386 KANK2 2.0 +s_27610 INSRR 2.0 +s_2769 AOC3 4.0 +s_58632 TRA2B 24.0 +s_6674 C16orf86 2.0 +s_22902 GJD4 2.0 +s_48278 RPS15A 2.0 +s_61998 WIPF2 2.0 +s_4937 BAIAP3 4.0 +s_54471 STOML1 4.0 +s_19157 FABP12 2.0 +s_5434 BIN1 4.0 +s_42042 PIP5K1A 2.0 +s_7794 C3orf18 2.0 +s_54846 SVIL 2.0 +s_62273 XPA 2.0 +s_45859 RACGAP1 2.0 +s_53626 SPOCK3 2.0 +s_43295 PPAP2C 14.0 +s_11788 CHRDL1 4.0 +s_50636 SHQ1 2.0 +s_16705 DPF1 2.0 +s_39741 OTOF 2.0 +s_27505 INHBE 2.0 +s_707 ACPL2 2.0 +s_15418 DDX3Y 12.0 +s_56018 TEAD4 2.0 +s_44367 PRR12 2.0 +s_25875 HOXB5 2.0 +s_49360 SCN9A 2.0 +s_16244 DMPK 2.0 +s_3909 ASCC2 2.0 +s_55088 SYT6 2.0 +s_54311 STAU1 2.0 +s_53890 SRP72 2.0 +s_11035 CDX1 2.0 +s_18178 EMR3 4.0 +s_16084 DLD 2.0 +s_47207 RHOBTB1 2.0 +s_40267 PARK2 12.0 +s_43104 POLR3B 2.0 +s_2200 AMDHD2 2.0 +s_12738 CNRIP1 2.0 +s_17842 EIF4A3 2.0 +s_57950 TMPRSS3 2.0 +s_62146 WRN 2.0 +s_11055 CEACAM1 2.0 +s_54580 STX2 2.0 +s_29277 KIAA1407 2.0 +s_33428 MEF2A 2.0 +s_59797 TUBB 2.0 +s_18113 EME1 2.0 +s_29839 KLHL8 2.0 +s_18058 ELP2 2.0 +s_49497 SDCBP2 6.0 +s_16874 DRP2 2.0 +s_13572 CREBL2 2.0 +s_20540 FBXO30 2.0 +s_64380 ZNF646 2.0 +s_50366 SH2B1 2.0 +s_2548 ANKRD33B 2.0 +s_41183 PDXP 2.0 +s_16315 DNAH12 2.0 +s_19996 FAM49B 2.0 +s_30751 LDLRAD3 2.0 +s_36960 NGEF 2.0 +s_39015 OR2A2 2.0 +s_26302 HSPB2 2.0 +s_64297 ZNF611 10.0 +s_730 ACSBG1 2.0 +s_50271 SFXN4 2.0 +s_8592 CA6 4.0 +s_13683 CRMP1 2.0 +s_51103 SLC16A7 2.0 +s_63785 ZNF384 2.0 +s_16339 DNAH9 2.0 +s_55936 TCTEX1D1 2.0 +s_14497 CXorf40A 2.0 +s_1123 ADAT1 2.0 +s_41304 PERP 2.0 +s_18719 ESAM 2.0 +s_35118 MSX2 2.0 +s_30128 KRT6A 2.0 +s_402 ABTB1 2.0 +s_32578 MAP1LC3A 2.0 +s_45063 PTMA 2.0 +s_43551 PPP1R14D 2.0 +s_2538 ANKRD32 2.0 +s_40384 PAX1 2.0 +s_29076 KIAA0101 2.0 +s_40482 PCDH10 2.0 +s_2348 ANGPT2 2.0 +s_59756 TTYH3 2.0 +s_34330 MOB4 2.0 +s_49331 SCN2B 2.0 +s_54905 SYDE1 2.0 +s_39101 OR2T1 2.0 +s_36623 NEDD4L 2.0 +s_40500 PCDH15 4.0 +s_10660 CDC42SE2 2.0 +s_30867 LGALS13 2.0 +s_24322 GSTK1 4.0 +s_59167 TRPC1 2.0 +s_57440 TMEM201 2.0 +s_50539 SHC1 2.0 +s_37087 NIT1 2.0 +s_56345 TGFB2 2.0 +s_55388 TARM1 2.0 +s_1224 ADD2 2.0 +s_5256 BCOR 4.0 +s_51731 SLC35B3 2.0 +s_12987 COL6A6 2.0 +s_56745 TJP3 2.0 +s_19340 FAM120AOS 2.0 +s_53904 SRPR 2.0 +s_1588 AGXT 2.0 +s_46157 RASA3 2.0 +s_19166 FABP3 14.0 +s_22330 GATM 2.0 +s_10731 CDH13 2.0 +s_2329 ANAPC5 2.0 +s_46045 RANGAP1 2.0 +s_54814 SUV39H2 2.0 +s_56169 TEX14 2.0 +s_3433 ARHGEF26 2.0 +s_48032 RP4-811H24.6 2.0 +s_51930 SLC41A3 2.0 +s_63893 ZNF433 2.0 +s_46996 RGCC 2.0 +s_13863 CSF3R 2.0 +s_26337 HSPH1 2.0 +s_12983 COL6A3 2.0 +s_1376 ADSS 2.0 +s_45449 PYHIN1 2.0 +s_49629 SEC22C 2.0 +s_20204 FAM86A 2.0 +s_24920 HDAC9 2.0 +s_14961 DAPK1 2.0 +s_23900 GPR98 4.0 +s_14485 CXorf27 2.0 +s_61808 WDR66 2.0 +s_55855 TCF7 2.0 +s_44652 PSG8 2.0 +s_46608 RCCD1 2.0 +s_61175 VCAM1 2.0 +s_27453 INCA1 2.0 +s_28987 KDM4C 2.0 +s_20613 FBXO7 2.0 +s_7715 C2orf70 6.0 +s_3902 ASB9 2.0 +s_64098 ZNF534 2.0 +s_31108 LIN7B 2.0 +s_3383 ARHGEF1 2.0 +s_7626 C2orf43 2.0 +s_52247 SLC8A1 2.0 +s_54498 STOX1 2.0 +s_12160 CLDN17 2.0 +s_16224 DMD 2.0 +s_41715 PHLDB2 2.0 +s_12197 CLDN7 2.0 +s_51239 SLC22A16 2.0 +s_41286 PEPD 2.0 +s_2367 ANGPTL4 2.0 +s_59289 TSC22D4 2.0 +s_22437 GCFC2 2.0 +s_24343 GSTO2 2.0 +s_32783 MAPKAPK5 2.0 +s_37032 NINJ1 2.0 +s_49065 SASH3 2.0 +s_60466 UGT1A1 2.0 +s_26043 HPSE2 4.0 +s_21199 FLNA 2.0 +s_41054 PDGFRA 2.0 +s_1820 AKNA 2.0 +s_19548 FAM166A 2.0 +s_43967 PRDX5 2.0 +s_51905 SLC39A8 2.0 +s_22723 GGT5 10.0 +s_13242 COX6C 2.0 +s_27668 IP6K1 2.0 +s_64491 ZNF692 2.0 +s_61982 WHSC1L1 4.0 +s_48495 RSAD1 2.0 +s_34351 MOCS3 2.0 +s_12069 CLCA1 6.0 +s_22023 GABRR1 2.0 +s_12812 COASY 4.0 +s_40068 PAIP1 2.0 +s_11513 CGREF1 4.0 +s_32119 LY6K 2.0 +s_60743 UQCR11 2.0 +s_56354 TGFBR1 2.0 +s_3062 APOL2 2.0 +s_20525 FBXO25 2.0 +s_55591 TBC1D7 2.0 +s_14987 DARS2 2.0 +s_63195 ZMAT2 2.0 +s_41936 PIK3C2G 2.0 +s_56092 TEP1 2.0 +s_61284 VIT 2.0 +s_10035 CCND2 2.0 +s_43744 PPP6R3 4.0 +s_48110 RPL10L 2.0 +s_39381 OR5H15 2.0 +s_6827 C17orf90 4.0 +s_8795 CADPS 2.0 +s_55301 TAF9 2.0 +s_25756 HNRNPM 2.0 +s_61177 VCAN 2.0 +s_22932 GLB1 2.0 +s_55751 TCEA2 2.0 +s_39419 OR5T3 2.0 +s_33669 MEX3A 2.0 +s_42714 PLXNC1 2.0 +s_23239 GNAT1 2.0 +s_4546 ATPAF1 2.0 +s_64432 ZNF671 2.0 +s_31346 LOXHD1 2.0 +s_46353 RBFOX2 2.0 +s_8848 CALHM2 2.0 +s_27039 IL12RB1 2.0 +s_62824 ZCCHC9 2.0 +s_7498 C20orf96 2.0 +s_43406 PPIE 2.0 +s_54925 SYN1 2.0 +s_27284 IL31RA 2.0 +s_63774 ZNF37A 2.0 +s_43643 PPP1R8 2.0 +s_63149 ZIC2 2.0 +s_26251 HSP90AB1 2.0 +s_46773 RELL2 2.0 +s_64868 ZP4 2.0 +s_626 ACLY 2.0 +s_40694 PCED1A 2.0 +s_15888 DHTKD1 2.0 +s_53641 SPP1 2.0 +s_21822 FXR1 2.0 +s_53660 SPR 2.0 +s_29906 KLKB1 2.0 +s_1901 ALAS2 2.0 +s_45130 PTPN2 2.0 +s_43535 PPP1R13B 4.0 +s_15855 DHRS12 2.0 +s_13602 CRH 2.0 +s_51848 SLC39A1 2.0 +s_61205 VDR 2.0 +s_18989 EXOC7 2.0 +s_22294 GATA1 4.0 +s_34584 MRAS 2.0 +s_33140 MCFD2 2.0 +s_34546 MPST 2.0 +s_27208 IL21R 2.0 +s_14576 CYB5R4 2.0 +s_43745 PPP6R3 2.0 +s_41675 PHF8 2.0 +s_41243 PEBP4 4.0 +s_42685 PLXNA1 2.0 +s_41585 PHB2 2.0 +s_47989 RP1L1 2.0 +s_42300 PLA2G6 2.0 +s_53387 SPATA6L 2.0 +s_15423 DDX4 2.0 +s_64039 ZNF506 10.0 +s_22276 GAS6 2.0 +s_15373 DDX19B 2.0 +s_4322 ATP2B2 2.0 +s_25787 HOMER1 2.0 +s_10739 CDH16 2.0 +s_51702 SLC34A3 2.0 +s_20623 FBXO9 4.0 +s_13244 COX6C 2.0 +s_35367 MTX2 2.0 +s_5681 BPIFB6 2.0 +s_57337 TMEM176A 2.0 +s_43464 PPM1F 2.0 +s_20530 FBXO28 2.0 +s_55958 TDGF1 2.0 +s_4516 ATP7B 2.0 +s_19128 F8 2.0 +s_40084 PAK1IP1 2.0 +s_29430 KIF20B 2.0 +s_14773 CYP46A1 2.0 +s_19102 F2R 2.0 +s_29306 KIAA1524 4.0 +s_11438 CETN3 2.0 +s_49647 SEC24D 2.0 +s_35891 NAA11 2.0 +s_10770 CDH23 4.0 +s_44838 PSMG2 2.0 +s_22687 GGCT 2.0 +s_14266 CTSW 2.0 +s_38451 NXF3 2.0 +s_60012 TYRP1 2.0 +s_13190 COTL1 2.0 +s_4721 AZI2 2.0 +s_28800 KCNMB3 2.0 +s_23136 GM2A 2.0 +s_31806 LRRC71 2.0 +s_11862 CHRNG 4.0 +s_52893 SNX12 2.0 +s_31960 LSM5 2.0 +s_3273 ARHGAP22 2.0 +s_22140 GALNT2 2.0 +s_36663 NEK1 2.0 +s_45974 RALB 2.0 +s_48582 RTCA 2.0 +s_27173 IL1RL1 2.0 +s_49800 SEMA6D 2.0 +s_18249 ENOPH1 2.0 +s_31609 LRRC10B 2.0 +s_6450 C14orf176 2.0 +s_42314 PLAC1L 2.0 +s_7822 C3orf27 2.0 +s_43695 PPP2R5C 2.0 +s_8939 CAMKV 2.0 +s_58681 TRAF7 2.0 +s_12850 COG6 2.0 +s_20936 FGF3 2.0 +s_10862 CDK17 2.0 +s_60046 UAP1 2.0 +s_42295 PLA2G5 2.0 +s_52045 SLC4A9 2.0 +s_18532 EPS8L3 2.0 +s_15737 DFNB31 2.0 +s_12691 CNOT4 2.0 +s_27651 INTS7 2.0 +s_52454 SLX4 2.0 +s_5507 BMF 2.0 +s_57583 TMEM25 2.0 +s_36267 NCK2 2.0 +s_15361 DDX17 2.0 +s_24303 GSS 2.0 +s_11095 CEBPB 4.0 +s_59318 TSG101 2.0 +s_35897 NAA16 2.0 +s_11714 CHMP3 2.0 +s_7217 C1orf186 2.0 +s_14282 CTU1 2.0 +s_53137 SOX15 2.0 +s_30977 LHX3 2.0 +s_825 ACTL6A 2.0 +s_33214 MCOLN3 2.0 +s_57706 TMEM55B 2.0 +s_41619 PHF12 2.0 +s_13595 CREM 2.0 +s_30523 LARP4 2.0 +s_6229 C11orf68 2.0 +s_17880 EIF4G2 2.0 +s_36676 NEK3 2.0 +s_23667 GPR123 2.0 +s_1296 ADORA1 2.0 +s_18235 ENHO 2.0 +s_20589 FBXO45 2.0 +s_31341 LOX 2.0 +s_20983 FGFR2 2.0 +s_44192 PRLR 2.0 +s_62014 WIPI2 2.0 +s_2585 ANKRD45 2.0 +s_14161 CTLA4 2.0 +s_63079 ZFYVE1 2.0 +s_7088 C1orf106 2.0 +s_10461 CD55 2.0 +s_24803 HBM 2.0 +s_52929 SNX21 2.0 +s_40041 PAFAH2 2.0 +s_17056 DUSP15 2.0 +s_61656 WDR12 2.0 +s_28830 KCNQ3 4.0 +s_44745 PSMB9 2.0 +s_16151 DLGAP5 2.0 +s_17799 EIF2S3 2.0 +s_49444 SCTR 2.0 +s_37203 NLGN3 2.0 +s_63798 ZNF385D 2.0 +s_42282 PLA2G4D 2.0 +s_27383 ILF3 2.0 +s_40974 PDE4DIP 2.0 +s_55037 SYT1 2.0 +s_52560 SMC6 2.0 +s_56910 TM9SF2 2.0 +s_64839 ZNHIT6 4.0 +s_20818 FES 2.0 +s_16789 DPY19L3 2.0 +s_46072 RAP2A 2.0 +s_24369 GTDC1 2.0 +s_5332 BEST3 2.0 +s_15793 DGKG 4.0 +s_13197 COX11 2.0 +s_1613 AHCYL1 2.0 +s_62445 YLPM1 2.0 +s_5441 BIN3 2.0 +s_20572 FBXO41 2.0 +s_26507 IBSP 2.0 +s_17166 DYNC2H1 2.0 +s_37694 NPNT 2.0 +s_62561 ZBP1 2.0 +s_28074 ITGB3BP 2.0 +s_13046 COMMD4 2.0 +s_4936 BAIAP3 2.0 +s_16345 DNAI1 4.0 +s_60141 UBE2D4 2.0 +s_34569 MPZL3 2.0 +s_35839 MYRIP 2.0 +s_42840 PNN 2.0 +s_64147 ZNF558 2.0 +s_21759 FUCA2 2.0 +s_62347 XYLB 2.0 +s_41049 PDGFD 2.0 +s_19760 FAM198B 2.0 +s_4944 BAMBI 2.0 +s_59471 TSSC1 2.0 +s_60224 UBE2T 2.0 +s_62753 ZC3H6 2.0 +s_29129 KIAA0355 2.0 +s_43266 PPA2 2.0 +s_48165 RPL31 2.0 +s_25918 HOXC8 2.0 +s_61309 VMO1 2.0 +s_29649 KLF5 2.0 +s_3093 APP 2.0 +s_59201 TRPM2 4.0 +s_31154 LIPH 2.0 +s_43571 PPP1R17 2.0 +s_58112 TNFRSF25 2.0 +s_22767 GHRL 2.0 +s_59817 TUBB6 2.0 +s_63192 ZMAT1 2.0 +s_7306 C1orf49 2.0 +s_37585 NOX5 2.0 +s_57817 TMEM87B 2.0 +s_3667 ARNTL2 2.0 +s_14264 CTSS 2.0 +s_61283 VIT 2.0 +s_35482 MXD3 4.0 +s_54197 STAC2 2.0 +s_54806 SUSD5 2.0 +s_22238 GAPT 2.0 +s_62113 WNT8A 2.0 +s_54543 STRN4 2.0 +s_33235 MDC1 2.0 +s_63489 ZNF224 2.0 +s_37914 NRG1 2.0 +s_36452 NDUFA3 2.0 +s_12262 CLEC3B 2.0 +s_25 AAAS 2.0 +s_50339 SGPP2 2.0 +s_30706 LDB1 2.0 +s_49357 SCN8A 2.0 +s_33618 METTL21D 2.0 +s_4402 ATP5O 2.0 +s_55017 SYNRG 2.0 +s_51299 SLC23A3 2.0 +s_34572 MR1 4.0 +s_49259 SCGB3A1 2.0 +s_17794 EIF2S1 2.0 +s_47977 RP11-744I24.1 2.0 +s_32701 MAP7 2.0 +s_32432 MAGI3 2.0 +s_36564 NDUFS6 2.0 +s_11527 CHAC1 2.0 +s_56181 TEX22 2.0 +s_714 ACPT 2.0 +s_51144 SLC18A1 2.0 +s_57122 TMEM117 2.0 +s_28872 KCTD1 2.0 +s_63600 ZNF28 2.0 +s_57369 TMEM182 2.0 +s_60388 UCK1 2.0 +s_47188 RHEB 2.0 +s_15237 DCTD 2.0 +s_42694 PLXNA4 2.0 +s_19680 FAM187B 2.0 +s_35378 MUC1 2.0 +s_38682 OGG1 2.0 +s_1085 ADAMTS9 2.0 +s_40910 PDE1A 2.0 +s_27956 ISOC2 2.0 +s_27821 IRAK1 2.0 +s_16210 DMBT1 2.0 +s_63398 ZNF184 2.0 +s_18679 ERMP1 2.0 +s_9161 CASC1 4.0 +s_45196 PTPRF 2.0 +s_23002 GLIS2 2.0 +s_17310 EBP 2.0 +s_54797 SUSD3 2.0 +s_1528 AGPAT4 2.0 +s_7045 C1QTNF6 2.0 +s_22952 GLCE 2.0 +s_7105 C1orf111 2.0 +s_36537 NDUFC1 2.0 +s_15359 DDX11 2.0 +s_32881 MARK3 2.0 +s_27486 INHA 2.0 +s_2399 ANK2 2.0 +s_60825 USP10 2.0 +s_20838 FEZ2 2.0 +s_43974 PREB 2.0 +s_16482 DNAJC5G 2.0 +s_26334 HSPG2 2.0 +s_46175 RASD1 2.0 +s_26764 IFT20 2.0 +s_14739 CYP2J2 2.0 +s_11386 CERS2 2.0 +s_5964 BTN1A1 2.0 +s_16810 DPYSL3 2.0 +s_16136 DLGAP2 2.0 +s_13401 CPPED1 2.0 +s_22359 GBGT1 2.0 +s_49575 SDSL 2.0 +s_62067 WNT16 2.0 +s_61863 WDR83OS 2.0 +s_44742 PSMB8 4.0 +s_31855 LRRFIP2 2.0 +s_528 ACADM 2.0 +s_13073 COPA 2.0 +s_32741 MAPK3 2.0 +s_38779 OPA3 2.0 +s_34827 MRPS17 2.0 +s_16969 DTX1 2.0 +s_56448 THAP4 2.0 +s_906 ACVR2A 2.0 +s_45078 PTP4A2 2.0 +s_23628 GPR101 2.0 +s_58510 TPD52L1 2.0 +s_561 ACAT2 2.0 +s_52492 SMAP2 2.0 +s_24039 GRB2 2.0 +s_46264 RASSF4 2.0 +s_39609 ORMDL3 2.0 +s_47343 RIMS4 2.0 +s_56575 THUMPD1 2.0 +s_3261 ARHGAP18 2.0 +s_8148 C6orf165 2.0 +s_17030 DUSP10 2.0 +s_56155 TEX101 2.0 +s_21191 FLI1 2.0 +s_50732 SIK1 2.0 +s_2914 APCDD1 2.0 +s_30717 LDB3 2.0 +s_4702 AXIN1 4.0 +s_21360 FNIP2 2.0 +s_54350 STEAP4 2.0 +s_57227 TMEM14A 4.0 +s_58177 TNIK 2.0 +s_7465 C20orf26 4.0 +s_17327 ECE2 2.0 +s_51639 SLC30A10 2.0 +s_4352 ATP5A1 2.0 +s_18616 ERCC8 2.0 +s_44043 PRIMA1 2.0 +s_36712 NELL2 2.0 +s_61348 VPS16 2.0 +s_2680 ANO4 2.0 +s_30437 LAMB2 2.0 +s_33742 MFSD12 2.0 +s_58796 TRHR 2.0 +s_52365 SLCO5A1 2.0 +s_41281 PEMT 2.0 +s_23427 GON4L 2.0 +s_13427 CPSF3L 2.0 +s_40193 PAPD7 2.0 +s_21543 FPGT 4.0 +s_16722 DPH2 2.0 +s_40078 PAIP2B 2.0 +s_60284 UBL5 2.0 +s_59936 TXNDC15 2.0 +s_31898 LRRTM4 2.0 +s_44833 PSMG1 4.0 +s_19552 FAM166B 2.0 +s_19478 FAM151A 2.0 +s_30185 KRTAP1-3 2.0 +s_61742 WDR45 2.0 +s_7252 C1orf212 2.0 +s_29507 KIF9 2.0 +s_2786 AP1G1 2.0 +s_21222 FLT1 2.0 +s_38408 NUP93 2.0 +s_60875 USP25 2.0 +s_39905 P2RX5 2.0 +s_54470 STOML1 2.0 +s_19064 EYA4 2.0 +s_41060 PDGFRL 2.0 +s_32049 LUC7L 2.0 +s_11837 CHRNA9 2.0 +s_64166 ZNF563 2.0 +s_11211 CENPK 2.0 +s_63097 ZFYVE21 2.0 +s_24757 HAUS4 2.0 +s_4190 ATG7 2.0 +s_48629 RTN4 2.0 +s_22880 GJB3 2.0 +s_44427 PRR7 2.0 +s_464 AC069154.2 2.0 +s_22093 GALC 2.0 +s_55367 TAPBP 2.0 +s_56672 TIMM22 2.0 +s_22286 GAS7 2.0 +s_45341 PVR 2.0 +s_34498 MPL 2.0 +s_60077 UBA7 6.0 +s_44215 PRMT5 2.0 +s_15576 DEFB125 2.0 +s_44098 PRKAR2B 6.0 +s_38270 NUDT19 2.0 +s_12662 CNNM3 2.0 +s_51149 SLC18A2 2.0 +s_42223 PKP4 2.0 +s_31072 LIMK1 2.0 +s_6339 C12orf53 2.0 +s_26400 HTR3E 2.0 +s_43315 PPARD 2.0 +s_28264 JAM3 2.0 +s_33927 MIER1 2.0 +s_11251 CEP104 2.0 +s_33388 MED24 2.0 +s_53844 SRGAP1 2.0 +s_40003 PACSIN2 2.0 +s_5428 BIK 2.0 +s_28459 KAZN 2.0 +s_12578 CNBP 2.0 +s_20731 FCRL3 2.0 +s_41692 PHKB 6.0 +s_13730 CRTC2 2.0 +s_50741 SIKE1 4.0 +s_10340 CD276 2.0 +s_42441 PLD6 2.0 +s_32600 MAP2K1 4.0 +s_21836 FXYD3 10.0 +s_33227 MCTP2 2.0 +s_23930 GPS1 2.0 +s_58948 TRIM46 2.0 +s_23579 GPER 2.0 +s_19158 FABP12 2.0 +s_26003 HPGD 2.0 +s_12701 CNOT7 2.0 +s_41164 PDS5B 2.0 +s_35675 MYLIP 2.0 +s_54071 SSX5 2.0 +s_59652 TTC9C 2.0 +s_35593 MYH10 2.0 +s_28060 ITGB1BP1 2.0 +s_52258 SLC8A3 4.0 +s_52898 SNX14 2.0 +s_25618 HMGCS1 2.0 +s_5068 BBS9 2.0 +s_4389 ATP5J 2.0 +s_49674 SEC62 2.0 +s_10264 CD1D 2.0 +s_20442 FBXL16 2.0 +s_11296 CEP41 2.0 +s_64923 ZSCAN22 2.0 +s_43954 PRDX3 2.0 +s_41735 PHOX2A 2.0 +s_33740 MFSD11 2.0 +s_2779 AP000892.1 2.0 +s_12703 CNOT7 2.0 +s_23338 GNMT 2.0 +s_14454 CXXC1 2.0 +s_49387 SCO1 2.0 +s_9124 CARD8 2.0 +s_42754 PML 4.0 +s_38814 OPRD1 2.0 +s_40024 PADI4 2.0 +s_29225 KIAA1147 2.0 +s_43402 PPID 2.0 +s_58669 TRAF3IP3 2.0 +s_59528 TTC17 2.0 +s_19114 F2RL3 2.0 +s_3339 ARHGAP35 2.0 +s_1522 AGPAT2 2.0 +s_33006 MBD2 2.0 +s_64149 ZNF558 2.0 +s_9791 CCDC69 2.0 +s_51442 SLC25A4 2.0 +s_59174 TRPC4 2.0 +s_37772 NQO2 2.0 +s_28649 KCNH8 2.0 +s_39896 P2RX3 2.0 +s_44644 PSG4 2.0 +s_51440 SLC25A39 2.0 +s_23954 GPSM3 2.0 +s_58911 TRIM36 2.0 +s_20632 FBXW12 2.0 +s_50149 SETMAR 2.0 +s_42606 PLK4 4.0 +s_55148 TAB1 2.0 +s_64628 ZNF772 2.0 +s_10616 CDC34 2.0 +s_38307 NUDT8 2.0 +s_23831 GPR35 2.0 +s_17055 DUSP15 2.0 +s_6922 C19orf44 2.0 +s_42494 PLEKHF2 2.0 +s_2104 ALPK1 2.0 +s_17640 EGFR 2.0 +s_37797 NR1H3 2.0 +s_23299 GNG3 2.0 +s_9517 CCDC125 2.0 +s_7562 C22orf42 2.0 +s_38149 NTNG1 2.0 +s_64633 ZNF774 2.0 +s_34420 MORN3 2.0 +s_56144 TET2 2.0 +s_18093 EMC6 2.0 +s_63835 ZNF410 2.0 +s_35521 MYBPC1 2.0 +s_64601 ZNF75D 2.0 +s_42105 PITX2 2.0 +s_39091 OR2M4 4.0 +s_1765 AKAP13 2.0 +s_6189 C11orf45 2.0 +s_63701 ZNF330 2.0 +s_28136 ITM2A 2.0 +s_56984 TMCO1 2.0 +s_49007 SAMSN1 2.0 +s_33654 METTL7A 4.0 +s_41626 PHF14 2.0 +s_34072 MLF1 2.0 +s_8880 CALR 2.0 +s_8738 CACNB4 2.0 +s_64012 ZNF496 2.0 +s_59206 TRPM3 2.0 +s_3971 ASIC5 2.0 +s_190 ABCC10 2.0 +s_41999 PIM1 2.0 +s_64465 ZNF684 2.0 +s_18728 ESD 2.0 +s_33786 MGA 2.0 +s_39611 OS9 2.0 +s_3484 ARID1B 2.0 +s_1238 ADH4 2.0 +s_53695 SPRTN 2.0 +s_23676 GPR126 2.0 +s_26052 HRAS 2.0 +s_36545 NDUFS1 2.0 +s_63208 ZMAT5 2.0 +s_2908 APC 2.0 +s_15119 DCAF8 2.0 +s_64395 ZNF655 2.0 +s_54556 STUB1 2.0 +s_10027 CCNC 2.0 +s_20178 FAM83C 2.0 +s_38266 NUDT17 2.0 +s_63517 ZNF233 2.0 +s_5435 BIN1 6.0 +s_13322 CPEB3 6.0 +s_19210 FAHD2A 2.0 +s_28276 JDP2 2.0 +s_38449 NXF1 2.0 +s_44619 PSEN1 2.0 +s_49290 SCMH1 2.0 +s_63232 ZMYM3 2.0 +s_47908 RP11-173D9.3 2.0 +s_51358 SLC25A18 2.0 +s_42513 PLEKHG5 2.0 +s_270 ABHD1 2.0 +s_58611 TPSG1 2.0 +s_45665 RAB33A 2.0 +s_35550 MYCL1 2.0 +s_55953 TCTN3 2.0 +s_39190 OR4D5 2.0 +s_64862 ZP2 2.0 +s_48451 RRM2 2.0 +s_44136 PRKCZ 2.0 +s_12532 CMTM1 2.0 +s_13958 CSPP1 2.0 +s_61437 VSIG1 2.0 +s_2427 ANKH 2.0 +s_48236 RPP25 2.0 +s_25248 HHIP 2.0 +s_49666 SEC61A2 4.0 +s_40916 PDE1C 2.0 +s_51267 SLC22A3 4.0 +s_45250 PTPRU 2.0 +s_54454 STMN2 2.0 +s_50448 SH3BP5 2.0 +s_35505 MYB 2.0 +s_34174 MMD2 2.0 +s_43046 POLR1D 2.0 +s_26919 IGSF1 2.0 +s_59350 TSKU 2.0 +s_52462 SMAD3 2.0 +s_44496 PRSS22 2.0 +s_12310 CLIC1 2.0 +s_60920 USP38 2.0 +s_42557 PLEKHO2 2.0 +s_37636 NPEPL1 2.0 +s_56222 TFAP2A 2.0 +s_46417 RBM22 2.0 +s_20477 FBXL6 2.0 +s_30504 LAPTM4A 2.0 +s_49873 4-Sep 2.0 +s_22231 GAPDH 2.0 +s_24866 HCRT 2.0 +s_26084 HRH4 2.0 +s_266 ABCG8 2.0 +s_31387 LPCAT1 2.0 +s_38114 NTF3 2.0 +s_13990 CST11 2.0 +s_24036 GRB14 2.0 +s_50585 SHISA4 2.0 +s_14163 CTNNA1 2.0 +s_1729 AK2 2.0 +s_62985 ZFHX3 2.0 +s_21318 FNBP1L 2.0 +s_13575 CREBRF 2.0 +s_5344 BET1 2.0 +s_49424 SCRN2 2.0 +s_31170 LIPN 2.0 +s_54781 SURF2 2.0 +s_51325 SLC25A1 2.0 +s_34136 MLNR 2.0 +s_31677 LRRC31 2.0 +s_53307 SPARCL1 2.0 +s_28022 ITGA7 2.0 +s_31356 LOXL3 2.0 +s_118 ABCA12 2.0 +s_12481 CLUL1 2.0 +s_40393 PAX3 2.0 +s_39614 OS9 2.0 +s_22342 GBA2 2.0 +s_1136 ADC 2.0 +s_10401 CD37 2.0 +s_4512 ATP7A 2.0 +s_10615 CDC27 2.0 +s_54497 STOX1 2.0 +s_46754 REG4 2.0 +s_20299 FAP 2.0 +s_63316 ZNF138 2.0 +s_42213 PKP2 2.0 +s_52161 SLC6A4 2.0 +s_60954 USP48 2.0 +s_14721 CYP2C9 2.0 +s_54067 SSX3 2.0 +s_42512 PLEKHG5 2.0 +s_32324 MAD2L1BP 2.0 +s_26149 HSD11B1L 2.0 +s_62941 ZFAND1 2.0 +s_306 ABHD16A 2.0 +s_42173 PKIG 2.0 +s_33499 MEOX1 2.0 +s_2639 ANKS1A 2.0 +s_9221 CASP4 4.0 +s_60951 USP48 2.0 +s_42487 PLEKHB2 2.0 +s_12463 CLTB 2.0 +s_17140 DYDC2 2.0 +s_15238 DCTD 2.0 +s_32766 MAPK8IP3 2.0 +s_6844 C18orf1 2.0 +s_29768 KLHL25 2.0 +s_58192 TNIP3 2.0 +s_26239 HSF4 2.0 +s_14209 CTRL 2.0 +s_7539 C22orf25 2.0 +s_21263 FMNL3 2.0 +s_56798 TLK1 2.0 +s_30163 KRT80 2.0 +s_28530 KCNAB1 2.0 +s_50079 SESN2 2.0 +s_17622 EGFL7 2.0 +s_27107 IL17RE 2.0 +s_61128 VASH2 2.0 +s_7629 C2orf44 2.0 +s_59045 TRIML2 2.0 +s_53186 SP110 2.0 +s_44696 PSMA8 2.0 +s_4081 ATAT1 2.0 +s_59776 TUBA3C 2.0 +s_26981 IKBKB 2.0 +s_11984 CINP 2.0 +s_38231 NUDT1 2.0 +s_34096 MLKL 2.0 +s_39703 OSM 2.0 +s_44761 PSMC4 2.0 +s_29844 KLK1 2.0 +s_46470 RBM43 2.0 +s_21735 FTSJ1 2.0 +s_54159 ST7L 2.0 +s_29161 KIAA0586 2.0 +s_62066 WNT11 2.0 +s_32768 MAPK9 2.0 +s_38834 OPTC 2.0 +s_27041 IL12RB2 2.0 +s_25301 HIGD1C 2.0 +s_48626 RTN4 2.0 +s_2191 AMBRA1 2.0 +s_64637 ZNF775 2.0 +s_24425 GTF2IRD1 4.0 +s_28025 ITGA7 2.0 +s_21739 FTSJ2 2.0 +s_56140 TET1 2.0 +s_18340 EOGT 2.0 +s_48335 RPS6KA1 2.0 +s_8918 CAMK2N1 2.0 +s_9126 CARD8 2.0 +s_34993 MSC 2.0 +s_62519 YY1AP1 2.0 +s_17754 EIF2B2 2.0 +s_3894 ASB7 2.0 +s_1366 ADRBK2 2.0 +s_63368 ZNF169 2.0 +s_33217 MCRS1 2.0 +s_791 ACSS3 2.0 +s_3070 APOL5 2.0 +s_158 ABCB4 2.0 +s_46169 RASAL2 2.0 +s_31573 LRP3 2.0 +s_15806 DGKQ 2.0 +s_3426 ARHGEF2 2.0 +s_22505 GDAP2 2.0 +s_43731 PPP4R4 2.0 +s_62463 YPEL3 2.0 +s_1351 ADRA2A 2.0 +s_58570 TPPP 2.0 +s_27563 INPP5K 2.0 +s_64662 ZNF783 2.0 +s_43701 PPP2R5D 2.0 +s_41032 PDE9A 2.0 +s_40077 PAIP2B 2.0 +s_55106 SYTL2 2.0 +s_36104 NAT1 2.0 +s_5659 BPIFA2 2.0 +s_24738 HAS3 2.0 +s_23688 GPR135 2.0 +s_44125 PRKCI 2.0 +s_42154 PKDCC 2.0 +s_52320 SLC9B2 2.0 +s_56287 TFF1 2.0 +s_26218 HSDL1 2.0 +s_48811 S100A14 2.0 +s_27403 IMMT 2.0 +s_44547 PRSS50 2.0 +s_13554 CREB3L3 2.0 +s_52812 SNRNP35 2.0 +s_9678 CCDC28B 2.0 +s_42982 POLD4 2.0 +s_9038 CAPN3 2.0 +s_24550 GYG1 2.0 +s_7927 C4orf19 2.0 +s_59893 TWF2 2.0 +s_21776 FUS 2.0 +s_38699 OLA1 2.0 +s_15466 DDX54 2.0 +s_57105 TMEM110 2.0 +s_47396 RIPPLY2 2.0 +s_29679 KLHDC3 2.0 +s_19864 FAM214B 2.0 +s_22859 GIT2 2.0 +s_63818 ZNF397 2.0 +s_62767 ZC3HAV1 2.0 +s_30390 LAD1 2.0 +s_54683 SULT1C3 2.0 +s_29008 KDM5D 2.0 +s_24721 HARS 2.0 +s_19875 FAM217A 2.0 +s_33598 METTL18 2.0 +s_43299 PPAPDC1B 2.0 +s_23606 GPM6A 2.0 +s_8917 CAMK2G 2.0 +s_7803 C3orf22 2.0 +s_52734 SNAP91 4.0 +s_46558 RBPJL 2.0 +s_44462 PRRT2 2.0 +s_30938 LHB 2.0 +s_33858 MIA2 2.0 +s_1394 AEN 2.0 +s_39870 OXSR1 2.0 +s_4906 BAG6 2.0 +s_16155 DLK2 2.0 +s_35274 MTMR4 2.0 +s_10518 CD81 2.0 +s_39057 OR2F2 2.0 +s_43913 PRDM16 2.0 +s_34638 MRPL1 2.0 +s_612 ACER3 2.0 +s_32740 MAPK3 2.0 +s_16130 DLGAP1 2.0 +s_15564 DEFB119 2.0 +s_41047 PDGFC 2.0 +s_30824 LEPRE1 2.0 +s_19702 FAM189B 2.0 +s_16740 DPM3 2.0 +s_13557 CREB3L4 2.0 +s_10008 CCNA1 2.0 +s_58486 TP73 2.0 +s_18717 ESAM 2.0 +s_63612 ZNF280D 2.0 +s_14187 CTNND2 2.0 +s_59449 TSPO2 2.0 +s_42709 PLXNB3 2.0 +s_39221 OR4M2 2.0 +s_49750 SEMA3F 2.0 +s_8476 C9orf3 2.0 +s_45561 RAB11A 2.0 +s_5542 BMP5 2.0 +s_1064 ADAMTS4 2.0 +s_5354 BET3L 2.0 +s_17631 EGFLAM 2.0 +s_36593 NEBL 2.0 +s_6085 C10orf2 2.0 +s_13428 CPSF3L 2.0 +s_25023 HECW1 2.0 +s_3641 ARMC9 2.0 +s_56315 TFPT 2.0 +s_3278 ARHGAP22 2.0 +s_49946 SERPINA1 2.0 +s_20760 FDFT1 2.0 +s_26065 HRCT1 2.0 +s_50473 SH3GL1 2.0 +s_22971 GLI1 2.0 +s_24638 H6PD 2.0 +s_40488 PCDH11X 2.0 +s_61210 VEGFB 2.0 +s_28841 KCNQ5 2.0 +s_43717 PPP3R1 2.0 +s_25342 HIRA 2.0 +s_57951 TMPRSS4 2.0 +s_34011 MITF 2.0 +s_54412 STK32B 2.0 +s_16037 DISC1 2.0 +s_51701 SLC34A3 2.0 +s_54291 STAT4 2.0 +s_24419 GTF2I 2.0 +s_45973 RALB 2.0 +s_28705 KCNJ6 2.0 +s_5581 BNIP1 2.0 +s_19856 FAM213A 2.0 +s_18308 ENTPD1 2.0 +s_59198 TRPM1 2.0 +s_21871 FZD10 2.0 +s_1850 AKR1C4 2.0 +s_6867 C18orf54 2.0 +s_35715 MYO18B 2.0 +s_22242 GAPVD1 2.0 +s_32713 MAP7D3 2.0 +s_49953 SERPINA12 2.0 +s_55916 TCP11 2.0 +s_56174 TEX19 2.0 +s_22072 GAL 2.0 +s_41033 PDE9A 2.0 +s_26471 HYAL3 2.0 +s_60244 UBE2Z 2.0 +s_12589 CNEP1R1 2.0 +s_29896 KLK8 2.0 +s_29769 KLHL26 2.0 +s_39346 OR5AP2 2.0 +s_15213 DCPS 2.0 +s_48577 RTBDN 2.0 +s_32146 LYAR 2.0 +s_26382 HTR3C 2.0 +s_33001 MBD1 2.0 +s_41972 PIK3R2 2.0 +s_33212 MCOLN3 2.0 +s_35423 MUL1 2.0 +s_7838 C3orf35 2.0 +s_51092 SLC16A4 2.0 +s_20336 FASTK 2.0 +s_33469 MEI1 2.0 +s_5549 BMP7 2.0 +s_2490 ANKRD16 2.0 +s_38674 OGFRL1 2.0 +s_26322 HSPBAP1 2.0 +s_31244 LMNA 2.0 +s_34063 MLC1 2.0 +s_15550 DEFB113 2.0 +s_52892 SNX12 2.0 +s_25799 HOOK2 2.0 +s_55486 TAX1BP1 2.0 +s_4351 ATP5A1 2.0 +s_49917 SERHL2 2.0 +s_46614 RCHY1 2.0 +s_62680 ZBTB7B 2.0 +s_49488 SDCBP 2.0 +s_21866 FYTTD1 2.0 +s_23092 GLTPD1 2.0 +s_10675 CDC73 2.0 +s_12764 CNTN2 2.0 +s_9223 CASP5 2.0 +s_38310 NUDT8 2.0 +s_7059 C1QTNF9B 2.0 +s_33162 MCM3AP 2.0 +s_8498 C9orf50 2.0 +s_16876 DSC1 2.0 +s_14370 CWH43 2.0 +s_22565 GDPD1 2.0 +s_4304 ATP1B4 2.0 +s_3600 ARMC10 2.0 +s_18120 EMID1 2.0 +s_21865 FYN 2.0 +s_60042 U2SURP 2.0 +s_13930 CSNK1G3 2.0 +s_6618 C16orf53 2.0 +s_26173 HSD17B12 2.0 +s_46035 RANBP3L 2.0 +s_13167 CORO2A 2.0 +s_10481 CD6 2.0 +s_4563 ATPIF1 2.0 +s_50071 SERTAD4 2.0 +s_39089 OR2M3 2.0 +s_58390 TOR1AIP2 2.0 +s_45132 PTPN2 2.0 +s_34536 MPPED2 2.0 +s_24336 GSTM5 2.0 +s_38670 OGFR 2.0 +s_4606 ATXN3 2.0 +s_5049 BBS12 2.0 +s_28134 ITM2A 2.0 +s_23612 GPN1 2.0 +s_16085 DLEC1 2.0 +s_2525 ANKRD28 2.0 +s_1792 AKAP7 2.0 +s_27701 IPO11 2.0 +s_25633 HMGN5 2.0 +s_33287 MDM4 2.0 +s_17847 EIF4E 2.0 +s_58327 TOMM34 2.0 +s_54101 ST3GAL3 2.0 +s_41507 PGLYRP3 2.0 +s_38705 OLAH 2.0 +s_7336 C1orf61 2.0 +s_34439 MOSPD3 2.0 +s_33343 MED12 2.0 +s_30145 KRT75 2.0 +s_7793 C3orf18 2.0 +s_13874 CSH2 2.0 +s_14274 CTTN 2.0 +s_38166 NTRK2 2.0 +s_2916 APCDD1L 2.0 +s_41582 PHB 2.0 +s_16033 DISC1 2.0 +s_54156 ST7L 2.0 +s_21942 GABARAPL1 2.0 +s_19312 FAM115C 2.0 +s_5431 BIN1 2.0 +s_44378 PRR15 2.0 +s_22113 GALNT1 2.0 +s_11744 CHN1 2.0 +s_13702 CROT 2.0 +s_14052 CT62 2.0 +s_28143 ITM2C 2.0 +s_43456 PPM1B 2.0 +s_1396 AES 2.0 +s_21931 GAB2 2.0 +s_39536 OR8J3 2.0 +s_62622 ZBTB37 2.0 +s_10417 CD3G 2.0 +s_23789 GPR176 2.0 +s_37011 NICN1 2.0 +s_55412 TAS1R2 2.0 +s_36626 NEDD4L 2.0 +s_62812 ZCCHC4 2.0 +s_18097 EMC7 2.0 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CELF4 0 +s_1116 ADARB1 0 +s_11218 CENPL 0 +s_11222 CENPM 0 +s_1127 ADAT2 0 +s_11294 CEP41 0 +s_11317 CEP63 0 +s_11456 CFH 0 +s_11585 CHD1 0 +s_11598 CHD3 0 +s_11692 CHL1 0 +s_1177 ADCY3 0 +s_1179 ADCY4 0 +s_1183 ADCY5 0 +s_11877 CHST13 0 +s_11928 CHUK 0 +s_12015 CITED1 0 +s_12019 CIZ1 0 +s_12021 CIZ1 0 +s_12049 CKLF-CMTM1 0 +s_12057 CKMT2 0 +s_12082 CLCC1 0 +s_12089 CLCF1 0 +s_1212 ADD1 0 +s_12120 CLCN7 0 +s_12121 CLCN7 0 +s_12138 CLDN10 0 +s_12140 CLDN10 0 +s_12177 CLDN2 0 +s_12187 CLDN25 0 +s_12203 CLDND1 0 +s_12209 CLDND2 0 +s_12420 CLPTM1 0 +s_12425 CLPX 0 +s_12433 CLRN2 0 +s_12522 CMPK2 0 +s_12576 CNBP 0 +s_12611 CNGB1 0 +s_12624 CNIH2 0 +s_12666 CNNM3 0 +s_12708 CNP 0 +s_12856 COG8 0 +s_12875 COL14A1 0 +s_12906 COL22A1 0 +s_12923 COL27A1 0 +s_13026 COLEC12 0 +s_13035 COMMD1 0 +s_13067 COMT 0 +s_13091 COPG1 0 +s_13123 COQ2 0 +s_13198 COX11 0 +s_13220 COX4I2 0 +s_13253 COX7A2L 0 +s_13287 CPA5 0 +s_13290 CPA6 0 +s_13309 CPE 0 +s_13328 CPED1 0 +s_13338 CPLX3 0 +s_13387 CPO 0 +s_13389 CPO 0 +s_13393 CPOX 0 +s_13405 CPS1 0 +s_13486 CR2 0 +s_13512 CRB1 0 +s_1357 ADRB1 0 +s_13579 CREBZF 0 +s_13662 CRK 0 +s_13686 CRMP1 0 +s_13718 CRTAM 0 +s_13755 CRYBA1 0 +s_13856 CSF3 0 +s_13857 CSF3 0 +s_13879 CSHL1 0 +s_1393 AEN 0 +s_13937 CSNK2A1 0 +s_13985 CSRP3 0 +s_14021 CSTA 0 +s_14099 CTCFL 0 +s_14107 CTD-2616J11.4 0 +s_14153 CTIF 0 +s_14189 CTNND2 0 +s_14226 CTSC 0 +s_14286 CTU2 0 +s_14338 CUTA 0 +s_14364 CWF19L1 0 +s_14369 CWH43 0 +s_14418 CXCL3 0 +s_14425 CXCL6 0 +s_14439 CXCR4 0 +s_14463 CXXC4 0 +s_14467 CXXC5 0 +s_1450 AGA 0 +s_14520 CXorf61 0 +s_14586 CYBA 0 +s_14670 CYP26A1 0 +s_14761 CYP3A4 0 +s_14894 DAB2IP 0 +s_14938 DALRD3 0 +s_14995 DAXX 0 +s_14996 DAXX 0 +s_15017 DBF4 0 +s_15052 DBP 0 +s_15113 DCAF6 0 +s_15182 DCLRE1A 0 +s_15320 DDI1 0 +s_15363 DDX17 0 +s_15385 DDX23 0 +s_15405 DDX31 0 +s_15438 DDX46 0 +s_15440 DDX47 0 +s_15472 DDX58 0 +s_15482 DDX6 0 +s_15488 DDX60L 0 +s_1549 AGPS 0 +s_1550 AGPS 0 +s_15520 DEF8 0 +s_15522 DEF8 0 +s_15563 DEFB119 0 +s_15566 DEFB119 0 +s_15586 DEFB127 0 +s_15648 DENND2D 0 +s_15655 DENND4A 0 +s_15679 DEPDC1 0 +s_15700 DERL1 0 +s_15731 DFFB 0 +s_15800 DGKI 0 +s_15867 DHRS3 0 +s_15897 DHX16 0 +s_15939 DHX40 0 +s_15965 DIAPH3 0 +s_15988 DIO1 0 +s_1599 AGXT2L1 0 +s_1609 AHCY 0 +s_16149 DLGAP5 0 +s_16175 DLX1 0 +s_16190 DLX3 0 +s_16294 DMXL2 0 +s_16341 DNAH9 0 +s_16417 DNAJC13 0 +s_16505 DNALI1 0 +s_16506 DNALI1 0 +s_16554 DNM2 0 +s_16577 DNMT3A 0 +s_16607 DOCK3 0 +s_1661 AIF1 0 +s_16629 DOCK8 0 +s_1663 AIF1L 0 +s_16675 DOPEY1 0 +s_16745 DPP10 0 +s_16798 DPYD 0 +s_16866 DRGX 0 +s_16867 DRGX 0 +s_1687 AIM1 0 +s_16878 DSC1 0 +s_16993 DUOX1 0 +s_17119 DUT 0 +s_17168 DYNC2LI1 0 +s_17195 DYRK1B 0 +s_17214 DYX1C1 0 +s_17224 DZIP1L 0 +s_17229 E2F1 0 +s_17374 ECT2 0 +s_17432 EDN2 0 +s_17440 EDNRA 0 +s_17442 EDNRB 0 +s_17459 EEF1D 0 +s_1766 AKAP14 0 +s_17709 EHMT2 0 +s_17762 EIF2B4 0 +s_1779 AKAP4 0 +s_17811 EIF3E 0 +s_17901 EIF5A2 0 +s_17942 ELF1 0 +s_17959 ELF5 0 +s_18018 ELOF1 0 +s_18106 EMCN 0 +s_18119 EMID1 0 +s_18125 EMILIN1 0 +s_18145 EML2 0 +s_18170 EMR1 0 +s_18171 EMR1 0 +s_18273 ENPP3 0 +s_1834 AKR1B10 0 +s_18362 EPB41L1 0 +s_18365 EPB41L1 0 +s_18409 EPHA10 0 +s_18423 EPHA4 0 +s_18445 EPHA8 0 +s_18531 EPS8L3 0 +s_18567 ERBB2IP 0 +s_18600 ERCC4 0 +s_18710 ERRFI1 0 +s_18739 ESM1 0 +s_18757 ESR2 0 +s_18767 ESRRA 0 +s_18772 ESRRB 0 +s_18782 ESYT1 0 +s_18809 ETHE1 0 +s_18849 ETV3 0 +s_18865 ETV4 0 +s_18908 EVL 0 +s_18920 EVX2 0 +s_18965 EXOC3L4 0 +s_19006 EXOSC3 0 +s_19048 EXTL2 0 +s_19126 F7 0 +s_19215 FAIM 0 +s_19254 FAM104A 0 +s_19255 FAM104B 0 +s_19499 FAM159A 0 +s_19605 FAM173B 0 +s_19614 FAM175B 0 +s_19633 FAM178A 0 +s_19664 FAM183A 0 +s_19674 FAM186A 0 +s_19699 FAM189B 0 +s_1971 ALDH8A1 0 +s_19728 FAM193A 0 +s_19736 FAM194A 0 +s_19744 FAM195B 0 +s_19747 FAM195B 0 +s_19859 FAM213B 0 +s_1992 ALG1 0 +s_200 ABCC2 0 +s_20007 FAM53A 0 +s_20077 FAM65B 0 +s_20080 FAM65C 0 +s_20106 FAM71B 0 +s_20116 FAM71E1 0 +s_20130 FAM73A 0 +s_20176 FAM83B 0 +s_2023 ALG3 0 +s_20269 FANCC 0 +s_20325 FAS 0 +s_2037 ALG9 0 +s_20377 FAXC 0 +s_20487 FBXO11 0 +s_2053 ALKBH4 0 +s_20616 FBXO7 0 +s_20635 FBXW2 0 +s_20686 FCGR1A 0 +s_20794 FEM1C 0 +s_20861 FGD1 0 +s_2092 ALOX5AP 0 +s_20946 FGF5 0 +s_21104 FIP1L1 0 +s_21231 FLT4 0 +s_21281 FMO4 0 +s_21342 FNDC5 0 +s_21375 FOLR1 0 +s_21504 FOXP1 0 +s_21627 FRMD8 0 +s_21642 FRRS1 0 +s_21650 FRS3 0 +s_21725 FTH1 0 +s_21736 FTSJ1 0 +s_21781 FUT10 0 +s_21813 FUZ 0 +s_21845 FXYD5 0 +s_21887 FZD8 0 +s_21895 G0S2 0 +s_21912 G6PC2 0 +s_21927 GAB1 0 +s_22006 GABRG2 0 +s_22033 GAD1 0 +s_2205 AMELX 0 +s_22151 GALNT5 0 +s_2226 AMIGO2 0 +s_22316 GATAD2A 0 +s_2238 AMMECR1L 0 +s_22485 GCNT2 0 +s_22537 GDF5 0 +s_22595 GEMIN5 0 +s_22608 GEMIN8 0 +s_22699 GGCX 0 +s_22715 GGPS1 0 +s_22741 GH1 0 +s_22810 GIMAP8 0 +s_2306 ANAPC11 0 +s_23236 GNAS 0 +s_23343 GNPDA1 0 +s_23423 GOLT1B 0 +s_23608 GPM6B 0 +s_23618 GPN3 0 +s_23683 GPR132 0 +s_2376 ANGPTL6 0 +s_23767 GPR161 0 +s_23963 GPT2 0 +s_23969 GPX2 0 +s_24129 GRIN2D 0 +s_24146 GRIP1 0 +s_24174 GRM3 0 +s_24199 GRM8 0 +s_24201 GRN 0 +s_24204 GRP 0 +s_24320 GSTCD 0 +s_24383 GTF2A2 0 +s_24430 GTF3C1 0 +s_24448 GTF3C5 0 +s_24533 GUK1 0 +s_2464 ANKRD10 0 +s_24644 HAAO 0 +s_24664 HADHB 0 +s_24741 HAT1 0 +s_24916 HDAC8 0 +s_24922 HDAC9 0 +s_24936 HDGF 0 +s_2497 ANKRD18A 0 +s_25016 HECTD3 0 +s_25027 HECW2 0 +s_2509 ANKRD23 0 +s_25157 HESX1 0 +s_25264 HHLA3 0 +s_25337 HIPK4 0 +s_25380 HIST1H2BC 0 +s_2539 ANKRD33 0 +s_25606 HMGCL 0 +s_25692 HNF1B 0 +s_25696 HNF4A 0 +s_25732 HNRNPCL1 0 +s_2579 ANKRD44 0 +s_2580 ANKRD44 0 +s_25914 HOXC6 0 +s_25988 HPD 0 +s_26064 HRC 0 +s_26290 HSPA8 0 +s_26388 HTR3D 0 +s_26556 ICT1 0 +s_26557 ICT1 0 +s_26805 IGDCC3 0 +s_26858 IGFBP4 0 +s_26862 IGFBP5 0 +s_26987 IKBKG 0 +s_27005 IKZF3 0 +s_27030 IL12A 0 +s_27046 IL13 0 +s_27111 IL17REL 0 +s_27114 IL18 0 +s_27146 IL1F10 0 +s_27151 IL1R1 0 +s_27183 IL1RN 0 +s_27202 IL20RB 0 +s_27215 IL22RA1 0 +s_27236 IL24 0 +s_27265 IL2RA 0 +s_27266 IL2RA 0 +s_2729 ANXA11 0 +s_27311 IL36G 0 +s_27324 IL37 0 +s_27330 IL4I1 0 +s_27332 IL4I1 0 +s_27347 IL6R 0 +s_27412 IMPA1 0 +s_27482 ING4 0 +s_27571 INS 0 +s_27580 INSIG1 0 +s_27604 INSM2 0 +s_27693 IP6K3 0 +s_27760 IQCF1 0 +s_27828 IRAK2 0 +s_27843 IRF1 0 +s_27868 IRF6 0 +s_27958 IST1 0 +s_27995 ITGA11 0 +s_28004 ITGA3 0 +s_2807 AP2A1 0 +s_28135 ITM2A 0 +s_28192 ITSN1 0 +s_28215 IYD 0 +s_2828 AP3B2 0 +s_28288 JMJD1C 0 +s_2837 AP3S1 0 +s_28436 KAT8 0 +s_28463 KAZN 0 +s_28510 KCNA10 0 +s_28650 KCNIP1 0 +s_28680 KCNJ13 0 +s_28725 KCNK10 0 +s_28742 KCNK16 0 +s_28750 KCNK18 0 +s_28834 KCNQ4 0 +s_29117 KIAA0284 0 +s_29140 KIAA0430 0 +s_29312 KIAA1598 0 +s_29387 KIF13A 0 +s_29471 KIF2B 0 +s_29554 KIRREL3 0 +s_29561 KISS1 0 +s_29590 KLC3 0 +s_29591 KLC4 0 +s_29627 KLF15 0 +s_2968 APLP1 0 +s_29735 KLHL18 0 +s_29841 KLHL8 0 +s_29843 KLHL9 0 +s_29897 KLK8 0 +s_299 ABHD14B 0 +s_30162 KRT8 0 +s_30215 KRTAP12-3 0 +s_30263 KRTAP26-1 0 +s_30311 KRTAP9-3 0 +s_30357 L3MBTL1 0 +s_30378 LACE1 0 +s_30446 LAMC1 0 +s_3051 APOF 0 +s_30538 LARP7 0 +s_30551 LAS1L 0 +s_30559 LAT 0 +s_30590 LBR 0 +s_3067 APOL3 0 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0 +s_32962 MATN3 0 +s_3297 ARHGAP26 0 +s_33017 MBD4 0 +s_3312 ARHGAP30 0 +s_33131 MCF2 0 +s_3317 ARHGAP30 0 +s_33192 MCM9 0 +s_33218 MCRS1 0 +s_33319 MECP2 0 +s_33476 MEIS2 0 +s_33561 METTL1 0 +s_33565 METTL11B 0 +s_33625 METTL23 0 +s_33723 MFNG 0 +s_33750 MFSD2B 0 +s_338 ABI1 0 +s_33812 MGAT4B 0 +s_33844 MGST1 0 +s_33885 MICAL3 0 +s_33958 MINA 0 +s_34151 MLXIPL 0 +s_34213 MMP2 0 +s_34226 MMP24 0 +s_34294 MNT 0 +s_34310 MOB1B 0 +s_3432 ARHGEF26 0 +s_3437 ARHGEF3 0 +s_34406 MORF4L2 0 +s_34464 MPDZ 0 +s_34474 MPHOSPH10 0 +s_34503 MPND 0 +s_34529 MPP7 0 +s_34624 MRI1 0 +s_34715 MRPL33 0 +s_34909 MRRF 0 +s_34918 MRVI1 0 +s_34944 MS4A14 0 +s_35008 MSH4 0 +s_35013 MSH4 0 +s_35139 MTA1 0 +s_35186 MTF1 0 +s_3526 ARL11 0 +s_35281 MTMR7 0 +s_35375 MUC1 0 +s_35396 MUC21 0 +s_35406 MUC4 0 +s_3544 ARL16 0 +s_35478 MXD1 0 +s_35480 MXD3 0 +s_35497 MXRA7 0 +s_35519 MYBPC1 0 +s_35569 MYD88 0 +s_35596 MYH11 0 +s_35682 MYLK 0 +s_35796 MYOF 0 +s_35811 MYOM3 0 +s_35836 MYPOP 0 +s_35923 NAA60 0 +s_35935 NAALADL2 0 +s_35964 NACC1 0 +s_35973 NADK 0 +s_36044 NANS 0 +s_36143 NAV2 0 +s_36222 NCAPH2 0 +s_36273 NCKAP1L 0 +s_36282 NCKAP5 0 +s_36286 NCKIPSD 0 +s_36335 NCR1 0 +s_36342 NCR3 0 +s_36351 NCS1 0 +s_36386 NDOR1 0 +s_36482 NDUFAF3 0 +s_3650 ARMCX4 0 +s_36519 NDUFB5 0 +s_3668 ARNTL2 0 +s_3670 ARPC1A 0 +s_36703 NELF 0 +s_36740 NEU1 0 +s_36825 NFATC2 0 +s_37035 NINJ1 0 +s_37048 NIPA1 0 +s_37084 NIT1 0 +s_37091 NIT2 0 +s_37103 NKAIN4 0 +s_37151 NKX2-5 0 +s_37222 NLRC4 0 +s_37258 NLRP3 0 +s_37274 NLRP7 0 +s_37286 NMB 0 +s_37326 NME7 0 +s_37384 NMUR1 0 +s_37407 NOA1 0 +s_37430 NODAL 0 +s_37438 NOL10 0 +s_37451 NOL4 0 +s_37502 NOS1 0 +s_37572 NOX1 0 +s_37579 NOX4 0 +s_37655 NPHP1 0 +s_37801 NR1H4 0 +s_37810 NR1I3 0 +s_37816 NR2C1 0 +s_37863 NR4A2 0 +s_37868 NR4A3 0 +s_3791 ARV1 0 +s_37945 NRL 0 +s_37963 NRP2 0 +s_37972 NRSN2 0 +s_37991 NRXN2 0 +s_38022 NSFL1C 0 +s_38097 NT5DC2 0 +s_38124 NTM 0 +s_3813 ASAP1 0 +s_38169 NTRK2 0 +s_38179 NTSR2 0 +s_38202 NUBP2 0 +s_38205 NUBPL 0 +s_38212 NUCB2 0 +s_38225 NUDCD2 0 +s_38305 NUDT7 0 +s_38336 NUMB 0 +s_3841 ASB11 0 +s_38429 NUSAP1 0 +s_38431 NUSAP1 0 +s_38516 NYX 0 +s_38525 OAS1 0 +s_38567 OBSL1 0 +s_38592 OCM2 0 +s_38602 ODAM 0 +s_38679 OGG1 0 +s_38683 OGG1 0 +s_38747 OLR1 0 +s_3881 ASB4 0 +s_38824 OPRM1 0 +s_38825 OPRM1 0 +s_38832 OPTC 0 +s_3888 ASB6 0 +s_38901 OR10W1 0 +s_38963 OR1A2 0 +s_39135 OR2T8 0 +s_39192 OR4D6 0 +s_39237 OR4X2 0 +s_39262 OR51F2 0 +s_3938 ASGR2 0 +s_39500 OR7D4 0 +s_39620 OSBP2 0 +s_39650 OSBPL3 0 +s_39654 OSBPL5 0 +s_39737 OTOA 0 +s_39747 OTOF 0 +s_39802 OTUD7A 0 +s_39865 OXSM 0 +s_39964 PABPC1 0 +s_39972 PABPC4 0 +s_39987 PACRGL 0 +s_40004 PACSIN2 0 +s_40016 PADI2 0 +s_40055 PAGE2B 0 +s_40089 PAK2 0 +s_40120 PALM 0 +s_40137 PAM 0 +s_40148 PAN2 0 +s_40156 PANK1 0 +s_40159 PANK2 0 +s_40182 PAOX 0 +s_40184 PAPD4 0 +s_40227 PAQR5 0 +s_4025 ASS1 0 +s_40261 PARD6B 0 +s_40269 PARK2 0 +s_40316 PARP3 0 +s_40392 PAX3 0 +s_40395 PAX3 0 +s_40397 PAX3 0 +s_4041 ASTN2 0 +s_40436 PBOV1 0 +s_40457 PCBD1 0 +s_40487 PCDH11X 0 +s_40510 PCDH19 0 +s_40521 PCDH7 0 +s_40597 PCDHB2 0 +s_40606 PCDHB8 0 +s_40925 PDE2A 0 +s_40936 PDE4A 0 +s_41027 PDE8B 0 +s_41077 PDIA2 0 +s_41084 PDIA4 0 +s_41138 PDLIM5 0 +s_41141 PDLIM7 0 +s_41145 PDP1 0 +s_41185 PDYN 0 +s_41279 PELP1 0 +s_41294 PER2 0 +s_41347 PEX19 0 +s_41439 PFN4 0 +s_41474 PGBD2 0 +s_41620 PHF13 0 +s_41701 PHKG2 0 +s_41772 PHYHIPL 0 +s_41807 PIAS1 0 +s_41879 PIGR 0 +s_41955 PIK3CD 0 +s_42051 PIP5KL1 0 +s_42055 PIP5KL1 0 +s_42068 PISD 0 +s_42081 PITPNC1 0 +s_4209 ATL2 0 +s_42107 PITX3 0 +s_42123 PJA1 0 +s_42148 PKD2L2 0 +s_42162 PKHD1L1 0 +s_42181 PKM 0 +s_42215 PKP3 0 +s_4224 ATN1 0 +s_42243 PLA2G16 0 +s_42261 PLA2G2E 0 +s_42292 PLA2G5 0 +s_42305 PLA2R1 0 +s_42321 PLAC8L1 0 +s_42351 PLB1 0 +s_42366 PLCB2 0 +s_42392 PLCH1 0 +s_42446 PLEC 0 +s_42467 PLEKHA5 0 +s_42519 PLEKHG6 0 +s_42536 PLEKHM1 0 +s_42544 PLEKHM3 0 +s_42554 PLEKHO1 0 +s_42560 PLEKHS1 0 +s_42616 PLOD1 0 +s_42663 PLSCR5 0 +s_42751 PML 0 +s_42792 PNCK 0 +s_42839 PNN 0 +s_42932 PODXL2 0 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R3HCC1L 0 +s_45566 RAB11FIP1 0 +s_45586 RAB11FIP5 0 +s_45600 RAB15 0 +s_45601 RAB15 0 +s_45604 RAB17 0 +s_45627 RAB24 0 +s_45707 RAB3C 0 +s_45729 RAB3IP 0 +s_45763 RAB6A 0 +s_45796 RAB9B 0 +s_45894 RAD51AP1 0 +s_45908 RAD51C 0 +s_45960 RAI14 0 +s_45961 RAI14 0 +s_46068 RAP1GDS1 0 +s_46107 RAPH1 0 +s_46265 RASSF4 0 +s_46298 RAVER2 0 +s_46321 RBBP5 0 +s_46328 RBBP7 0 +s_46355 RBFOX3 0 +s_46452 RBM39 0 +s_46581 RCAN1 0 +s_46634 RCOR2 0 +s_46639 RCSD1 0 +s_46646 RD3 0 +s_46657 RDH10 0 +s_46672 RDH13 0 +s_46717 REEP1 0 +s_46821 RERG 0 +s_46827 RERGL 0 +s_46848 RETNLB 0 +s_46976 RFXANK 0 +s_47005 RGL2 0 +s_4703 AXIN1 0 +s_47100 RGS3 0 +s_47144 RHAG 0 +s_47186 RHD 0 +s_47216 RHOC 0 +s_47394 RIPPLY1 0 +s_47413 RLBP1 0 +s_47554 RNF130 0 +s_47584 RNF144A 0 +s_47594 RNF145 0 +s_47622 RNF165 0 +s_47710 RNF215 0 +s_47777 RNF44 0 +s_47780 RNF6 0 +s_47786 RNF7 0 +s_47791 RNF8 0 +s_47915 RP11-178D12.1 0 +s_47946 RP11-428C6.1 0 +s_47969 RP11-6F2.7 0 +s_47970 RP11-6F2.7 0 +s_48013 RP4-697K14.7 0 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TCP11 0 +s_55922 TCP11L2 0 +s_55946 TCTN1 0 +s_56006 TEAD2 0 +s_56014 TEAD4 0 +s_56080 TEN1 0 +s_56099 TERF1 0 +s_56118 TES 0 +s_56167 TEX13B 0 +s_5618 BOK 0 +s_56207 TEX9 0 +s_56284 TFEC 0 +s_56297 TFG 0 +s_56361 TGFBR2 0 +s_56373 TGIF1 0 +s_56415 TGS1 0 +s_56492 THEM4 0 +s_56509 THNSL1 0 +s_5655 BPIFA1 0 +s_56621 TIFA 0 +s_56646 TIMD4 0 +s_56684 TIMM8B 0 +s_56805 TLL1 0 +s_56819 TLR10 0 +s_56826 TLR3 0 +s_56873 TM4SF18 0 +s_57016 TMED10 0 +s_57082 TMEM106C 0 +s_57087 TMEM107 0 +s_57150 TMEM127 0 +s_57173 TMEM132B 0 +s_57181 TMEM132E 0 +s_57189 TMEM134 0 +s_57288 TMEM164 0 +s_57299 TMEM167B 0 +s_57409 TMEM194A 0 +s_57422 TMEM198 0 +s_57429 TMEM2 0 +s_57475 TMEM212 0 +s_57531 TMEM231 0 +s_57568 TMEM245 0 +s_57700 TMEM54 0 +s_57873 TMF1 0 +s_57992 TMUB1 0 +s_58180 TNIP1 0 +s_58211 TNKS2 0 +s_58237 TNNT1 0 +s_58256 TNPO2 0 +s_58259 TNPO3 0 +s_58309 TOM1 0 +s_58485 TP73 0 +s_58503 TPD52 0 +s_58533 TPI1 0 +s_5857 BSPRY 0 +s_58612 TPSG1 0 +s_58633 TRA2B 0 +s_58655 TRAF3 0 +s_58668 TRAF3IP2 0 +s_58690 TRAK1 0 +s_58809 TRIB2 0 +s_58962 TRIM50 0 +s_58968 TRIM52 0 +s_59050 TRIO 0 +s_59107 TRMT1L 0 +s_59133 TRMT61B 0 +s_59160 TROVE2 0 +s_59173 TRPC4 0 +s_59196 TRPM1 0 +s_59204 TRPM3 0 +s_59311 TSEN54 0 +s_59332 TSHB 0 +s_59340 TSHZ2 0 +s_59360 TSNARE1 0 +s_5952 BTG4 0 +s_59539 TTC21A 0 +s_59602 TTC39A 0 +s_59654 TTC9C 0 +s_59717 TTLL6 0 +s_5974 BTN3A1 0 +s_59748 TTYH1 0 +s_59807 TUBB2B 0 +s_59859 TULP1 0 +s_59870 TULP3 0 +s_59955 TXNDC8 0 +s_59983 TXNRD2 0 +s_600 ACE 0 +s_60169 UBE2H 0 +s_60209 UBE2Q2 0 +s_60237 UBE2V2 0 +s_60248 UBE3A 0 +s_60250 UBE3B 0 +s_60373 UBXN6 0 +s_60396 UCKL1 0 +s_60423 UEVLD 0 +s_60438 UFSP1 0 +s_60449 UGDH 0 +s_60517 UGT2A1 0 +s_60542 UGT3A1 0 +s_60603 UMODL1 0 +s_60614 UNC119 0 +s_60649 UNC5B 0 +s_6068 C10orf125 0 +s_6071 C10orf128 0 +s_60753 UQCRC2 0 +s_60780 URM1 0 +s_60839 USP15 0 +s_60851 USP19 0 +s_60925 USP4 0 +s_6100 C10orf53 0 +s_6106 C10orf54 0 +s_61149 VAV2 0 +s_61173 VCAM1 0 +s_61178 VCAN 0 +s_61221 VEPH1 0 +s_61263 VIL1 0 +s_61341 VPS13C 0 +s_61344 VPS13D 0 +s_61367 VPS29 0 +s_61529 VWA5A 0 +s_61531 VWA5A 0 +s_61587 WBP1 0 +s_61595 WBP2 0 +s_61623 WDFY1 0 +s_61640 WDHD1 0 +s_61662 WDR16 0 +s_61695 WDR26 0 +s_61739 WDR44 0 +s_6200 C11orf49 0 +s_62019 WISP1 0 +s_62098 WNT5B 0 +s_62114 WNT8A 0 +s_62171 WTAP 0 +s_62249 XKR3 0 +s_62257 XKR6 0 +s_62275 XPC 0 +s_62320 XRCC4 0 +s_62361 YAE1D1 0 +s_62550 ZBBX 0 +s_62559 ZBED6 0 +s_62567 ZBTB1 0 +s_62624 ZBTB37 0 +s_62657 ZBTB47 0 +s_62759 ZC3H7A 0 +s_62845 ZDHHC11 0 +s_62862 ZDHHC16 0 +s_62881 ZDHHC2 0 +s_6292 C12orf23 0 +s_62975 ZFC3H1 0 +s_63034 ZFP64 0 +s_63104 ZFYVE27 0 +s_63107 ZFYVE27 0 +s_63114 ZFYVE28 0 +s_63217 ZMIZ2 0 +s_63228 ZMYM3 0 +s_63234 ZMYM3 0 +s_6326 C12orf49 0 +s_63302 ZNF132 0 +s_63362 ZNF167 0 +s_63435 ZNF200 0 +s_63487 ZNF223 0 +s_63594 ZNF276 0 +s_636 ACO1 0 +s_63746 ZNF354B 0 +s_63755 ZNF362 0 +s_6376 C12orf74 0 +s_63903 ZNF436 0 +s_63905 ZNF438 0 +s_63923 ZNF442 0 +s_63934 ZNF445 0 +s_63935 ZNF446 0 +s_63964 ZNF469 0 +s_63983 ZNF480 0 +s_6409 C14orf105 0 +s_64137 ZNF554 0 +s_64241 ZNF586 0 +s_6427 C14orf133 0 +s_64356 ZNF639 0 +s_64393 ZNF655 0 +s_64396 ZNF655 0 +s_64419 ZNF668 0 +s_64424 ZNF669 0 +s_64459 ZNF682 0 +s_64479 ZNF688 0 +s_64581 ZNF746 0 +s_64627 ZNF772 0 +s_64638 ZNF776 0 +s_64652 ZNF780A 0 +s_64791 ZNF85 0 +s_64851 ZNRF3 0 +s_64871 ZPBP 0 +s_64878 ZPLD1 0 +s_64898 ZSCAN10 0 +s_64930 ZSCAN30 0 +s_64997 ZYG11A 0 +s_6525 C15orf39 0 +s_6592 C16orf13 0 +s_6639 C16orf62 0 +s_6707 C17orf102 0 +s_6710 C17orf104 0 +s_6728 C17orf112 0 +s_6736 C17orf39 0 +s_6794 C17orf72 0 +s_6814 C17orf80 0 +s_6849 C18orf21 0 +s_6859 C18orf32 0 +s_6862 C18orf34 0 +s_6906 C19orf38 0 +s_7053 C1QTNF7 0 +s_7128 C1orf122 0 +s_7144 C1orf130 0 +s_7162 C1orf144 0 +s_7234 C1orf198 0 +s_7341 C1orf63 0 +s_747 ACSL1 0 +s_76 AARS2 0 +s_7674 C2orf57 0 +s_7681 C2orf62 0 +s_7692 C2orf63 0 +s_77 AARSD1 0 +s_78 AARSD1 0 +s_781 ACSS1 0 +s_786 ACSS2 0 +s_7940 C4orf26 0 +s_7970 C4orf37 0 +s_8000 C4orf52 0 +s_804 ACTB 0 +s_8073 C5orf51 0 +s_8141 C6orf162 0 +s_8227 C7orf10 0 +s_8281 C7orf59 0 +s_8318 C8A 0 +s_8403 C9orf100 0 +s_8470 C9orf24 0 +s_8699 CACNA1G 0 +s_8705 CACNA1I 0 +s_871 ACTR8 0 +s_874 ACTR8 0 +s_8757 CACNG5 0 +s_8797 CADPS 0 +s_8879 CALR 0 +s_8910 CAMK2B 0 +s_893 ACVR1B 0 +s_8930 CAMKK1 0 +s_8954 CAMSAP1 0 +s_9064 CAPRIN1 0 +s_9077 CAPSL 0 +s_9109 CARD17 0 +s_913 ACY1 0 +s_9171 CASD1 0 +s_9196 CASP10 0 +s_9285 CATSPER3 0 +s_9506 CCDC120 0 +s_9507 CCDC121 0 +s_952 ADAM12 0 +s_9584 CCDC149 0 +s_964 ADAM18 0 +s_9646 CCDC170 0 +s_9710 CCDC40 0 +s_9732 CCDC48 0 +s_976 ADAM21 0 +s_9763 CCDC62 0 +s_9868 CCDC89 0 +s_991 ADAM30 0 +s_9925 CCL1 0 +s_9973 CCL26 0 diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/output_countsummary.Rnw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_countsummary.Rnw Wed Apr 04 11:03:59 2018 -0400 @@ -0,0 +1,237 @@ +% This is a template file for Sweave used in MAGeCK +% Author: Wei Li, Shirley Liu lab +% Do not modify lines beginning with "#__". +\documentclass{article} + +\usepackage{amsmath} +\usepackage{amscd} +\usepackage[tableposition=top]{caption} +\usepackage{ifthen} +\usepackage{fullpage} +\usepackage[utf8]{inputenc} +% \usepackage{longtable} + +\begin{document} +\setkeys{Gin}{width=0.9\textwidth} + +\title{MAGeCK Count Report} +\author{Wei Li} + +\maketitle + + +\tableofcontents + +\section{Summary} + +%Function definition +<>= +genreporttable<-function(filelist,labellist,reads,mappedreads){ + xtb=data.frame(Label=labellist,Reads=reads,MappedReads=mappedreads,MappedPercentage=mappedreads/reads); + colnames(xtb)=c("Label","Reads","Mapped","Percentage"); + return (xtb); +} +genreporttable2<-function(filelist,labellist,sgrnas,zerocounts,gini){ + xtb=data.frame(Label=labellist,TotalsgRNAs=sgrnas,ZeroCounts=zerocounts,GiniIndex=gini); + colnames(xtb)=c("Label","TotalsgRNA","ZeroCounts","GiniIndex"); + return (xtb); +} +genreporttable3<-function(filelist,labellist){ + xtb=data.frame(File=filelist,Label=labellist); + colnames(xtb)=c("File","Label"); + return (xtb); +} + + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F"); + + + +genboxplot<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + + boxplot(slmat_log,pch='.',las=2,ylab='log2(read counts)',cex.axis=0.8,...) +} + + +genhistplot<-function(filename,isfile=T,...){ + if(isfile){ + slmed=read.table(filename,header=T) + }else{ + slmed=filename; + } + tabsmat=as.matrix(log2(slmed[,c(-1,-2)]+1)) + colnames(tabsmat)=colnames(slmed)[c(-1,-2)] + samplecol=colors[((1:ncol(tabsmat)) %% length(colors)) ] + if(ncol(tabsmat)>=1){ + histlist=lapply(1:ncol(tabsmat),function(X){ return (hist(tabsmat[,X],plot=F,breaks=40)) }) + xrange=range(unlist(lapply(histlist,function(X){X$mids}))) + yrange=range(unlist(lapply(histlist,function(X){X$counts}))) + hst1=histlist[[1]] + plot(hst1$mids,hst1$counts,type='b',pch=20,xlim=c(0,xrange[2]*1.2),ylim=c(0,yrange[2]*1.2),xlab='log2(counts)',ylab='Frequency',main='Distribution of read counts',col = samplecol[1], ... ) + } + if(ncol(tabsmat)>=2){ + for(i in 2:ncol(tabsmat)){ + hstn=histlist[[i]] + lines(hstn$mids,hstn$counts,type='b',pch=20,col=samplecol[i]) + } + } + legend('topright',colnames(tabsmat),pch=20,lwd=1,col=samplecol) +} + + + +genclustering<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + + result=tryCatch({ + library(gplots); + heatmap.2(cor(slmat_log),trace = 'none',density.info = 'none',cexRow = 0.8,cexCol = 0.8,offsetRow = -0.2,offsetCol = -0.2) + }, error=function(e){ + heatmap(cor(slmat_log),scale='none',cexRow = 0.8,cexCol = 0.8,cex.axis=0.8,...) + }); +} + +ctfit_tx=0; + + +panel.plot<-function(x,y,textnames=names(x),...){ + par(new=TRUE) + m<-cbind(x,y) + plot(m,pch=20,xlim = range(x)*1.1,ylim=range(y)*1.1,...) + text(x,y,textnames,...) +} + + +genpcaplot<-function(filename,...){ + #slmed=read.table(filename,header=T) + slmed=read.table(filename,header=T) + slmat=as.matrix(slmed[,c(-1,-2)]) + slmat_log=log2(slmat+1) + ctfit_tx<<-prcomp(t(slmat_log),center=TRUE) + + # par(mfrow=c(2,1)); + samplecol=colors[((1:ncol(slmat)) %% length(colors)) ] + # first 2 PCA + #plot(ctfit_tx$x[,1],ctfit_tx$x[,2],xlab='PC1',ylab='PC2',main='First 2 PCs',col=samplecol,xlim=1.1*range(ctfit_tx$x[,1]),ylim=1.1*range(ctfit_tx$x[,2])); + #text(ctfit_tx$x[,1],ctfit_tx$x[,2],rownames(ctfit_tx$x),col=samplecol); + # par(mfrow=c(1,1)); + if(length(samplecol)>2){ + pairs(ctfit_tx$x[,1:3],panel=panel.plot,textnames=rownames(ctfit_tx$x),main='First 3 principle components',col=samplecol) + }else{ + if(length(samplecol)>1){ + pairs(ctfit_tx$x[,1:2],panel=panel.plot,textnames=rownames(ctfit_tx$x),main='First 2 principle components',col=samplecol) + } + } + + +} + +genpcavar<-function(){ + # % variance + varpca=ctfit_tx$sdev^2 + varpca=varpca/sum(varpca)*100; + if(length(varpca)>10){ + varpca=varpca[1:10]; + } + plot(varpca,type='b',lwd=2,pch=20,xlab='PCs',ylab='% Variance explained'); +} + +@ + +%__FILE_SUMMARY__ + +The statistics of comparisons are listed in Table 1 and Table 2. +The corresponding fastq files in each row are listed in Table 3. + +<>= +library(xtable) +filelist=c("input_0.gz"); +labellist=c("test1_fastq_gz"); +reads=c(2500); +mappedreads=c(1453); +totalsgrnas=c(2550); +zerocounts=c(1276); +giniindex=c(0.5266899931488773); + +cptable=genreporttable(filelist,labellist,reads,mappedreads); +print(xtable(cptable, caption = "Summary of comparisons", label = "tab:one", + digits = c(0, 0, 0, 0,2), + align=c('c', 'c','c', 'c', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + +<>= +library(xtable) +cptable=genreporttable2(filelist,labellist,totalsgrnas,zerocounts,giniindex); +print(xtable(cptable, caption = "Summary of comparisons", label = "tab:two", + digits = c(0, 0,0, 0,2), + align=c('c', 'c','c', 'c', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + + + + + +<>= +library(xtable) +cptable=genreporttable3(filelist,labellist); +print(xtable(cptable, caption = "Summary of samples", label = "tab:three", + digits = c(0,0, 0), + align=c('c', 'p{9cm}', 'c'), + table.placement = "tbp", + caption.placement = "top")) +@ + + + + +The meanings of the columns are as follows. + +\begin{itemize} +\item \textbf{Row}: The row number in the table; +\item \textbf{File}: The filename of fastq file; +\item \textbf{Label}: Assigned label; +\item \textbf{Reads}: The total read count in the fastq file; +\item \textbf{Mapped}: Reads that can be mapped to gRNA library; +\item \textbf{Percentage}: The percentage of mapped reads; +\item \textbf{TotalsgRNAs}: The number of sgRNAs in the library; +\item \textbf{ZeroCounts}: The number of sgRNA with 0 read counts; +\item \textbf{GiniIndex}: The Gini Index of the read count distribution. Gini index can be used to measure the evenness of the read counts, and a smaller value means a more even distribution of the read counts. +\end{itemize} + + + +\newpage\section{Normalized read count distribution of all samples} +The following figure shows the distribution of median-normalized read counts in all samples. + + +<>= +genboxplot("output.count_normalized.txt"); +@ + +The following figure shows the histogram of median-normalized read counts in all samples. + + +<>= +genhistplot("output.count_normalized.txt"); +@ + +%__INDIVIDUAL_PAGE__ + + + +\end{document} + diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/output_summary.Rnw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_summary.Rnw Wed Apr 04 11:03:59 2018 -0400 @@ -0,0 +1,1063 @@ +% This is a template file for Sweave used in MAGeCK +% Author: Wei Li, Shirley Liu lab +% Do not modify lines beginning with "#__". +\documentclass{article} + +\usepackage{amsmath} +\usepackage{amscd} +\usepackage[tableposition=top]{caption} +\usepackage{ifthen} +\usepackage{fullpage} +\usepackage[utf8]{inputenc} + +\begin{document} +\setkeys{Gin}{width=0.9\textwidth} + +\title{MAGeCK Comparison Report} +\author{Wei Li} + +\maketitle + + +\tableofcontents + +\section{Summary} + +%Function definition +<>= +genreporttable<-function(comparisons,ngenes,direction,fdr1,fdr5,fdr25){ + xtb=data.frame(Comparison=comparisons,Genes=ngenes,Selection=direction,FDR1=fdr1,FDR5=fdr5,FDR25=fdr25); + colnames(xtb)=c("Comparison","Genes","Selection","FDR1%","FDR5%","FDR25%"); + return (xtb); +} +@ + +The statistics of comparisons is as indicated in the following table. + +<>= +library(xtable) +comparisons=c("HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial neg.","HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial pos."); +ngenes=c(100,100); +direction=c("negative","positive"); +fdr1=c(0,0); +fdr5=c(2,0); +fdr25=c(9,1); + +cptable=genreporttable(comparisons,ngenes,direction,fdr1,fdr5,fdr25); +print(xtable(cptable, caption = "Summary of comparisons", label = "tab:one", + digits = c(0, 0, 0, 0, 0, 0, 0), + table.placement = "tbp", + caption.placement = "top")) +@ + +The meanings of the columns are as follows. + +\begin{itemize} +\item \textbf{Comparison}: The label for comparisons; +\item \textbf{Genes}: The number of genes in the library; +\item \textbf{Selection}: The direction of selection, either positive selection or negative selection; +\item \textbf{FDR1\%}: The number of genes with FDR $<$ 1\%; +\item \textbf{FDR5\%}: The number of genes with FDR $<$ 5\%; +\item \textbf{FDR25\%}: The number of genes with FDR $<$ 25\%; +\end{itemize} + +The following figures show: + +\begin{itemize} +\item Individual sgRNA read counts of selected genes in selected samples; +\item The distribution of RRA scores and p values of all genes; and +\item The RRA scores and p values of selected genes. +\end{itemize} + + +\newpage\section{Comparison results of HL60 final,KBM7 final vs HL60 initial,KBM7 initial neg.} + +The following figure shows the distribution of RRA score in the comparison HL60 final,KBM7 final vs HL60 initial,KBM7 initial neg., and the RRA scores of 10 genes. + +<>= +gstable=read.table('output.gene_summary.txt',header=T) +@ +% + + +<>=# +# +# parameters +# Do not modify the variables beginning with "__" + +# gstablename='__GENE_SUMMARY_FILE__' +startindex=3 +# outputfile='__OUTPUT_FILE__' +targetgenelist=c("ACIN1","ACTR8","AHCY","ACLY","AATF","AGBL5","AHCTF1","ABT1","ADIRF","ABCF1") +# samplelabel=sub('.\w+.\w+$','',colnames(gstable)[startindex]); +samplelabel='HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial neg.' + + +# You need to write some codes in front of this code: +# gstable=read.table(gstablename,header=T) +# pdf(file=outputfile,width=6,height=6) + + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + +###### +# function definition + +plotrankedvalues<-function(val, tglist, ...){ + + plot(val,log='y',ylim=c(max(val),min(val)),type='l',lwd=2, ...) + if(length(tglist)>0){ + for(i in 1:length(tglist)){ + targetgene=tglist[i]; + tx=which(names(val)==targetgene);ty=val[targetgene]; + points(tx,ty,col=colors[(i %% length(colors)) ],cex=2,pch=20) + # text(tx+50,ty,targetgene,col=colors[i]) + } + legend('topright',tglist,pch=20,pt.cex = 2,cex=1,col=colors) + } +} + + + +plotrandvalues<-function(val,targetgenelist, ...){ + # choose the one with the best distance distribution + + mindiffvalue=0; + randval=val; + for(i in 1:20){ + randval0=sample(val) + vindex=sort(which(names(randval0) %in% targetgenelist)) + if(max(vindex)>0.9*length(val)){ + # print('pass...') + next; + } + mindiffind=min(diff(vindex)); + if (mindiffind > mindiffvalue){ + mindiffvalue=mindiffind; + randval=randval0; + # print(paste('Diff: ',mindiffvalue)) + } + } + plot(randval,log='y',ylim=c(max(randval),min(randval)),pch=20,col='grey', ...) + + if(length(targetgenelist)>0){ + for(i in 1:length(targetgenelist)){ + targetgene=targetgenelist[i]; + tx=which(names(randval)==targetgene);ty=randval[targetgene]; + points(tx,ty,col=colors[(i %% length(colors)) ],cex=2,pch=20) + text(tx+50,ty,targetgene,col=colors[i]) + } + } + +} + + + + +# set.seed(1235) + + + +pvec=gstable[,startindex] +names(pvec)=gstable[,'id'] +pvec=sort(pvec); + +plotrankedvalues(pvec,targetgenelist,xlab='Genes',ylab='RRA score',main=paste('Distribution of RRA scores in \n',samplelabel)) + +# plotrandvalues(pvec,targetgenelist,xlab='Genes',ylab='RRA score',main=paste('Distribution of RRA scores in \n',samplelabel)) + + +pvec=gstable[,startindex+1] +names(pvec)=gstable[,'id'] +pvec=sort(pvec); + +plotrankedvalues(pvec,targetgenelist,xlab='Genes',ylab='p value',main=paste('Distribution of p values in \n',samplelabel)) + +# plotrandvalues(pvec,targetgenelist,xlab='Genes',ylab='p value',main=paste('Distribution of p values in \n',samplelabel)) + + + +# you need to write after this code: +# dev.off() + + + + +@ +%% +\clearpage +\newpage +The following figures show the distribution of sgRNA read counts (normalized) of selected genes in selected samples. +% + + +<>= +par(mfrow=c(2,2)); + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(561.4907165816957,824.0396348113272,428.37415340969943,579.047491896501),c(3424.79939695118,3818.2871009576584,1992.3498917052,690.0506672205338),c(846.6456878299913,985.6508562937211,335.0024675413113,415.97581680707134),c(2432.636481525409,2122.257249136931,1067.465489792653,155.6333179800872),c(1308.1851773762019,2186.1913587343615,1482.5909580453515,997.3120339679854),c(405.68439208520414,268.16807081144486,170.34023773287015,109.85881269182627),c(640.8637498157573,559.4234589775174,711.6436598617687,632.2603542941043),c(946.5969148654764,470.6260845366416,663.0651476194316,457.74505288260946),c(246.9383256170808,177.59474888175154,28.39003962214503,0.0),c(568.8400715107754,612.7018836420428,564.0154538266146,270.64176251684285)) +targetgene="ACIN1" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(2484.0819660289676,2349.578527705573,2172.7843657481662,910.9126552363929),c(992.1629154257711,1005.1862786707138,743.8190381001997,200.26346063614164),c(1267.0287897733551,1156.1418152202027,251.09412821363824,42.34141739164138),c(1500.738276518092,1315.977089213779,800.5991173444897,1476.2277955464156),c(1925.5309914189038,2054.7712445618654,194.94493873872918,235.16652091844063),c(351.29916561001374,781.4168950797068,227.75120674654121,624.2498158686586),c(1719.74905340467,1006.9622261595313,356.45271970026533,222.0063506480656),c(903.9706562768137,1445.6212558974576,1482.5909580453515,1055.1023468944147),c(651.152846716469,1081.552020689867,576.0023594448536,1072.2677863775127),c(285.1549712482957,408.46792242802854,99.0496937928171,44.630142656054424)) +targetgene="ACTR8" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(301.3235520922712,657.1005708624807,228.38209651592223,137.32351586478285),c(1142.0897559789987,1099.311495578042,112.92926871919911,100.70391163417409),c(789.3207193831689,671.3081507730209,723.6305654800077,588.7745742702564),c(392.45555321286054,412.0198174056636,334.37157777193033,213.99581222261992),c(2009.3136376104133,2235.917888421252,2437.1271791188055,1937.9781176417478),c(1071.5359486598327,406.69197493921104,645.4002340767636,349.602784139093),c(61.7345814042702,218.44154112455442,614.4866353770946,452.5954210376801),c(651.152846716469,879.0940069646701,237.21455328725622,18.88198343140764),c(1625.6773103124485,1410.1023061211074,2146.286995434164,1986.613529510525),c(1053.8974968300413,882.6459019423052,106.6203710253891,105.85354347910344)) +targetgene="AHCY" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(1268.498660759171,1411.8782536099247,1136.2324746551822,603.6512884889412),c(327.78122983695846,454.642557137284,51.73296108924205,24.031615276336996),c(132.28838872343613,241.5288584791821,123.02350502929512,65.80085135187511),c(495.34652221997754,586.0626713097802,279.4841678357833,243.74924065998954),c(1009.8013672555626,1102.8633905556771,1237.174837756142,1004.7503910773278),c(877.5129785321263,715.7068379934587,538.1489732819936,594.496387431289),c(1594.8100196103135,1108.1912330221296,605.6541786057605,127.59643349102738),c(314.5523909646148,252.1845434120872,88.95545748272109,359.9020478289517),c(512.984974049769,269.94401830026237,205.67006481820619,126.45207085882086),c(761.3931706526657,475.9539270030942,559.5992254409475,596.7851126957021)) +targetgene="ACLY" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +par(mfrow=c(1,1)); +@ +% + + +<>= +par(mfrow=c(2,2)); + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(659.9720726313648,809.832054900787,880.7221180558769,802.1982051767731),c(724.6463960072668,1086.8798631563195,695.2405258578626,307.26136674745163),c(836.3565909292796,1289.3378768815162,468.75109865008346,177.94838930811443),c(367.46774645398926,571.85509139924,300.30353022535627,116.72498848506541),c(518.8644579930328,632.2373060190355,627.7353205340956,308.9779106957614),c(405.68439208520414,259.28833336735727,324.27734146183434,166.5047629860492),c(2096.0360257735547,1960.6460276545372,1573.4390848362154,629.9716290296913),c(277.8056163192159,435.1071347602913,182.32714335110919,0.0),c(995.1026573974029,477.7298744919117,728.0467938656747,275.21921304566894),c(2185.6981559083283,1482.9161531626255,1741.8866532609427,1862.4501839161173)) +targetgene="AATF" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(640.8637498157573,602.0461987091378,307.2433176885473,192.82510352679924),c(354.23890758164566,280.5997032331675,204.4082852794442,275.79139436177223),c(779.0316224824572,932.3724316291956,778.5179754161547,905.1908420753603),c(624.6951689717818,554.0956165110648,370.96318439602834,558.4489645167836),c(1133.270530064103,1394.1187787217498,639.0913363829536,1131.2024619361487),c(423.32284391499564,412.0198174056636,224.59675789963623,426.84726181303336),c(296.91393913482335,829.3674772777797,489.5704610396565,1233.0507362025292),c(684.959879390236,546.9918265557948,394.30610586312537,566.4595029422292),c(440.96129574478715,630.461358530218,434.6830511035094,457.1728715665062),c(1108.2827233052317,1969.5257650986248,1066.2037102538911,1333.7546478367033)) +targetgene="AGBL5" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(196.96271209933826,301.9110730989776,423.9579250240324,34.33087896619571),c(1106.8128523194157,1056.6887558464218,1743.1484327997048,807.3478370217025),c(748.1643317803222,488.3855594248168,239.73811236478022,477.77139894622366),c(1095.053884432888,882.6459019423052,837.8216137379688,365.05167967388104),c(677.6105244611563,316.11865300951774,613.8557456077136,819.3636446598709),c(1078.8853035889126,1609.008424868669,348.88204246769334,193.96946615900578),c(1437.533824128006,1095.759600600407,320.4920028455483,161.35513114111984),c(845.1758168441753,660.6524658401157,541.3034221288985,640.8430740356532),c(551.2016196809839,740.570102836904,1103.42620664737,622.5332719203489),c(601.1772331987264,900.4053768304803,735.6174710982467,754.1349746240991)) +targetgene="AHCTF1" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(487.9971672908978,367.6211301852257,312.2904358435953,441.15179471561487),c(358.6485205390935,394.2603425174884,593.0363832181406,268.35303725242983),c(1743.266989177725,1980.1814500315297,837.1907239685878,281.5132075228048),c(1597.7497615819454,1465.1566782744503,1065.57282048451,992.7345834391593),c(119.05954985109253,378.2768151181308,185.48159219801417,128.7407961232339),c(986.2834314825072,745.8979453033566,328.0626800781203,302.11173490252224),c(523.2740709504807,694.3954681276485,336.89513684945433,597.9294753279087),c(1562.4728579223624,763.6574201915316,422.0652557158894,220.28980669975581),c(30.8672907021351,179.37069637056908,238.47633282601822,184.81456510135357),c(339.5401977234861,447.5387671820139,310.3977665354523,205.98527379717427)) +targetgene="ABT1" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +par(mfrow=c(1,1)); +@ +% + + +<>= +par(mfrow=c(2,2)); + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(492.4067802483456,221.99343610218943,309.7668767660713,102.99263689858714),c(243.9985836454489,239.7529109903646,130.59418226186713,174.51530141149487),c(734.9354929079785,673.0840982618383,620.7955330709046,470.9052231529845),c(1074.4756906314647,950.1319065173708,1100.902647569846,743.8357109342404),c(702.5983312200275,1010.5141211371663,1291.4313579229083,1017.3383800315995),c(1647.7253750996879,760.1055252138966,685.7771793171477,608.2287390177673),c(951.0065278229242,864.8864270541301,606.9159581445226,769.0116888427839),c(435.0818118015233,435.1071347602913,275.69882921949727,339.8757017653375),c(89.66213013477338,209.56180368046682,208.8245136651112,304.4004601669353),c(1328.7633711776252,1571.7135276035012,1122.983789498181,1356.6419004808338)) +targetgene="ADIRF" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(216.0710349149457,289.479440677255,192.42137966120518,498.36992632594104),c(1127.391046120839,1198.764554951823,371.5940741654094,370.2013115188104),c(1111.2224652768637,1038.9292809582466,948.227323379644,922.3562815584581),c(1164.137820766238,1204.0923974182756,1686.9992433247955,2089.033985093009),c(48.505742531926586,248.63264843445216,665.5887066969557,248.8988725049189),c(501.2260061632414,387.1565525622184,436.5757204116524,314.69972385679404),c(1975.5066049366465,1797.2588586833258,1628.3264947723626,1289.6966864967521),c(213.13129294331378,376.5008676293133,404.4003421732214,482.921030791153),c(2012.2533795820452,1989.0611874756173,1064.3110409457481,431.9968936579627),c(264.57677744687226,353.4135502746856,442.25372833608145,191.6807408945927)) +targetgene="ABCF1" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +par(mfrow=c(1,1)); +@ + +\newpage\section{Comparison results of HL60 final,KBM7 final vs HL60 initial,KBM7 initial pos.} + +The following figure shows the distribution of RRA score in the comparison HL60 final,KBM7 final vs HL60 initial,KBM7 initial pos., and the RRA scores of 10 genes. + +<>= +gstable=read.table('output.gene_summary.txt',header=T) +@ +% + + +<>=# +# +# parameters +# Do not modify the variables beginning with "__" + +# gstablename='__GENE_SUMMARY_FILE__' +startindex=9 +# outputfile='__OUTPUT_FILE__' +targetgenelist=c("ACRC","AGAP3","ADCK4","AHRR","ADRBK1","ADK","ADCK1","ADARB2","ACSS2","ADNP") +# samplelabel=sub('.\w+.\w+$','',colnames(gstable)[startindex]); +samplelabel='HL60_final,KBM7_final_vs_HL60_initial,KBM7_initial pos.' + + +# You need to write some codes in front of this code: +# gstable=read.table(gstablename,header=T) +# pdf(file=outputfile,width=6,height=6) + + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + +###### +# function definition + +plotrankedvalues<-function(val, tglist, ...){ + + plot(val,log='y',ylim=c(max(val),min(val)),type='l',lwd=2, ...) + if(length(tglist)>0){ + for(i in 1:length(tglist)){ + targetgene=tglist[i]; + tx=which(names(val)==targetgene);ty=val[targetgene]; + points(tx,ty,col=colors[(i %% length(colors)) ],cex=2,pch=20) + # text(tx+50,ty,targetgene,col=colors[i]) + } + legend('topright',tglist,pch=20,pt.cex = 2,cex=1,col=colors) + } +} + + + +plotrandvalues<-function(val,targetgenelist, ...){ + # choose the one with the best distance distribution + + mindiffvalue=0; + randval=val; + for(i in 1:20){ + randval0=sample(val) + vindex=sort(which(names(randval0) %in% targetgenelist)) + if(max(vindex)>0.9*length(val)){ + # print('pass...') + next; + } + mindiffind=min(diff(vindex)); + if (mindiffind > mindiffvalue){ + mindiffvalue=mindiffind; + randval=randval0; + # print(paste('Diff: ',mindiffvalue)) + } + } + plot(randval,log='y',ylim=c(max(randval),min(randval)),pch=20,col='grey', ...) + + if(length(targetgenelist)>0){ + for(i in 1:length(targetgenelist)){ + targetgene=targetgenelist[i]; + tx=which(names(randval)==targetgene);ty=randval[targetgene]; + points(tx,ty,col=colors[(i %% length(colors)) ],cex=2,pch=20) + text(tx+50,ty,targetgene,col=colors[i]) + } + } + +} + + + + +# set.seed(1235) + + + +pvec=gstable[,startindex] +names(pvec)=gstable[,'id'] +pvec=sort(pvec); + +plotrankedvalues(pvec,targetgenelist,xlab='Genes',ylab='RRA score',main=paste('Distribution of RRA scores in \n',samplelabel)) + +# plotrandvalues(pvec,targetgenelist,xlab='Genes',ylab='RRA score',main=paste('Distribution of RRA scores in \n',samplelabel)) + + +pvec=gstable[,startindex+1] +names(pvec)=gstable[,'id'] +pvec=sort(pvec); + +plotrankedvalues(pvec,targetgenelist,xlab='Genes',ylab='p value',main=paste('Distribution of p values in \n',samplelabel)) + +# plotrandvalues(pvec,targetgenelist,xlab='Genes',ylab='p value',main=paste('Distribution of p values in \n',samplelabel)) + + + +# you need to write after this code: +# dev.off() + + + + +@ +%% +\clearpage +\newpage +The following figures show the distribution of sgRNA read counts (normalized) of selected genes in selected samples. +% + + +<>= +par(mfrow=c(2,2)); + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(461.5394895462105,502.5931393353569,445.40817718298644,889.1697652244688),c(76.43329126242978,90.5733219296933,447.30084649112945,357.0411412484354),c(258.6972935036084,685.515730683561,533.7327448963265,560.7376897811967),c(232.23961575892122,681.9638357059259,275.69882921949727,467.47213525636494),c(1393.4376945535273,1472.2604682297203,1039.706339939889,532.7008052921368),c(2395.88970688001,2441.927797124084,2462.9936596634266,2461.5240218762324),c(495.34652221997754,605.5980936867728,1159.575396122279,1617.5565806239213),c(682.0201374186041,822.2636873225097,1572.1773052974536,1333.7546478367033),c(961.2956247236359,1097.5355480892247,959.5833392285019,905.1908420753603),c(1940.2297012770634,1289.3378768815162,942.5493154552149,1103.737758763192)) +targetgene="ACRC" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(1387.5582106102636,1120.6228654438523,1214.4628060584262,1111.1761158725344),c(388.0459402554127,509.69692929062694,933.0859689144999,750.1297054113762),c(326.3113588511425,635.7892009966705,960.8451187672639,615.6670961271097),c(1328.7633711776252,1038.9292809582466,1346.3187678590552,1596.3858719281006),c(352.7690365958297,234.42506852391205,310.3977665354523,429.1359870774464),c(693.7791053051318,678.4119407282909,784.1959833405838,895.4637597016048),c(837.8264619150956,719.2587329710938,374.74852301231437,993.8789460713658),c(365.99787546817333,369.3970776740432,333.74068800254935,746.6966175147567),c(707.0079441774753,635.7892009966705,837.1907239685878,1465.3563505404536),c(486.5272963050818,673.0840982618383,784.8268731099647,734.6808098765882)) +targetgene="AGAP3" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(830.4771069860158,864.8864270541301,1349.4732167059603,740.974804353724),c(1481.6299537024847,1994.38902994207,2044.082852794442,1810.9538654668238),c(1234.6916280854039,1299.9935618144214,1357.6747837079133,2232.6514954349277),c(224.89026082984142,188.25043381465665,700.2876440129107,81.24974688666317),c(812.8386551562243,845.3510046771374,946.334654071501,999.6007592323984),c(1978.4463469082782,1751.0842239740703,2659.2003779409174,2851.1794981425537),c(565.9003295391435,776.0890526132542,878.1985589783528,445.72924524444096),c(680.5502664327881,534.5601941340722,550.7667686696135,1025.9210997731484),c(161.68580843975528,333.87812789769293,275.0679394501163,465.18340999195186),c(2523.768482645998,2445.4796921017187,2153.226782897355,1516.8526689897471)) +targetgene="ADCK4" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(345.4196816667499,163.38716897121142,474.42910657451245,481.2044868428432),c(415.9734889859159,372.9489726516783,212.6098522813972,349.03060282298975),c(1.469870985815957,83.46953197442323,0.0,62.9399447713588),c(351.29916561001374,150.9555365494888,288.9475143764983,416.54799812317464),c(561.4907165816957,170.49095892648148,199.3611671243962,411.97054759434855),c(251.34793857452865,221.99343610218943,1564.6066280648815,1502.5481360871656),c(736.4053638937945,893.3015868752103,1114.782222496228,459.46159683091923),c(338.07032673767014,607.3740411755903,378.5338616286004,65.22867003577186),c(1230.2820151279561,525.6804566899846,837.1907239685878,945.2435342025885)) +targetgene="AHRR" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +par(mfrow=c(1,1)); +@ +% + + +<>= +par(mfrow=c(2,2)); + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(371.87735941143717,877.3180594758527,2395.4884543396593,1564.9158995424211),c(1109.7525942910477,1138.3823403320275,970.308465307979,999.0285779162951),c(1462.5216308868773,1209.420239884728,1537.4783679814984,1519.14139425416),c(586.4785233405669,987.4268037825386,743.8190381001997,1312.0117578247794),c(1018.6205931704583,717.4827854822763,1070.619938639558,1144.3626322065236),c(1269.9685317449869,1212.9721348623632,1591.1039983788835,1624.9949377332637),c(1321.4140162485455,1795.4829111945082,1478.8056194290655,1237.056005415252),c(908.3802692342615,832.9193722554148,1639.6825106212207,1268.5259778009315),c(923.078979092421,758.3295777250792,1479.4365091984464,1275.964334910274),c(680.5502664327881,634.013253507853,318.5993335374053,631.1159916618979)) +targetgene="ADRBK1" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(1472.810727787589,1829.225913482041,1263.0413183007631,1315.444845721399),c(208.7216799858659,65.71005708624807,292.1019632234033,350.17496545519623),c(1011.2712382413785,1166.7975001531076,652.9709113093356,860.5606994193058),c(557.0811036242477,685.515730683561,875.0441101314478,1019.6271052960126),c(363.0581334965414,825.8155823001447,736.8792506370087,349.602784139093),c(1505.14788947554,451.09066215964896,653.6018010787167,991.0180394908496),c(198.43258308515422,28.41515982108025,249.83234867487624,114.43626322065236),c(438.02155377315523,74.58979453033565,254.87946682992424,231.16125170571777),c(804.0194292413286,472.4020320254591,1336.2245315489592,1203.2973077651598),c(454.19013461713075,490.1615069136343,896.4943622904019,685.4732166917076)) +targetgene="ADK" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(662.9118146029966,1008.7381736483488,1101.533537339227,1694.8010582978616),c(1547.7741480642028,1965.9738701209897,1869.9572764452857,2353.9539344488194),c(1459.5818889152454,1179.2291325748304,1296.4784760779562,1222.1792911965672),c(1193.5352404825571,1355.0479339677643,1622.0175970785526,1905.9359639399652),c(868.6937526172306,701.4992580829187,720.4761166331027,603.6512884889412),c(798.1399452980647,768.9852626579842,1478.8056194290655,1756.0244591209105),c(1168.5474337236858,907.5091667857504,879.4603385171149,977.8578692204745),c(809.8989131845924,687.2916781723785,678.8373918539567,865.7103312642352),c(1246.4505959719315,753.0017352586266,1301.5255942330043,1264.5207085882087),c(826.0674940285679,797.4004224790644,977.8791425405509,2066.7189137649816)) +targetgene="ADCK1" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(1863.7964100146337,1585.9211075140413,1761.4442361117538,1464.211987908247),c(742.2848478370584,598.4943037315028,943.8110949939769,820.5080072920774),c(1568.3523418656262,2083.1864043829455,1810.6536381234716,1887.6261618246608),c(1018.6205931704583,513.248824268262,679.4682816233377,824.5132765048003),c(1140.6198849931827,1191.6607649965529,880.0912282864958,977.8578692204745),c(135.22813069506805,118.98848175077354,351.40560154521734,399.95473995618005),c(665.8515565746286,701.4992580829187,986.7115993118849,746.6966175147567),c(418.9132309575478,300.1351256101601,376.6411923204574,645.4205245644794),c(561.4907165816957,543.4399315781598,881.9838975946388,580.7640358448108),c(442.4311667306031,229.0972260574595,395.5678854018874,651.142337725512)) +targetgene="ADARB2" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +par(mfrow=c(1,1)); +@ +% + + +<>= +par(mfrow=c(2,2)); + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(734.9354929079785,358.74139274113816,541.9343118982795,378.7840312603593),c(595.2977492554626,591.3905137762326,1061.787481868224,887.4532212761591),c(1655.0747300287676,943.0281165621008,1069.358159100796,2038.1098479598186),c(626.1650399575977,884.4218494311227,517.3296108924205,858.2719741548927),c(680.5502664327881,747.673892792174,533.1018551269456,1016.194017399393),c(662.9118146029966,777.8650001020718,864.9498738213518,787.3214909580882),c(880.4527205037583,621.5816210861304,671.8976043907657,1040.7978139918332),c(94.07174309222125,447.5387671820139,711.6436598617687,927.5059134033875),c(399.80490814194036,806.280159923152,1147.58849050404,1059.1076161071376),c(698.1887182625796,531.0082991564371,504.0809257354195,347.8862401907832)) +targetgene="ACSS2" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +# parameters +# Do not modify the variables beginning with "__" +targetmat=list(c(408.62413405683606,523.9045092011671,483.89245311522745,701.494293542599),c(1805.0015705819953,1434.9655709645526,1712.2348341000356,2152.546111180471),c(3017.64513388016,2642.609863360463,1834.6274493599499,3573.2723190648703),c(1649.1952460855039,783.1928425685244,773.4708572611067,1332.0381038883936),c(959.82575373782,1397.6706736993847,1429.5962174173474,2811.126806015325),c(495.34652221997754,301.9110730989776,336.89513684945433,555.015876620164),c(1491.9190506031964,1331.9606166131366,2087.614246881731,1983.1804416139055),c(429.2023278582595,889.7496918975753,567.8007924429005,1132.9190058844583),c(427.7324568724435,573.6310388880576,655.4944703868597,899.4690289143276),c(690.8393633334998,767.2093151691668,1040.33722970927,993.3067647552625)) +targetgene="ADNP" +collabel=c("HL60_initial","KBM7_initial","HL60_final","KBM7_final") + +# set up color using RColorBrewer +#library(RColorBrewer) +#colors <- brewer.pal(length(targetgenelist), "Set1") + +colors=c( "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", + "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3", + "#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", + "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") + + +## code + +targetmatvec=unlist(targetmat)+1 +yrange=range(targetmatvec[targetmatvec>0]); +# yrange[1]=1; # set the minimum value to 1 +for(i in 1:length(targetmat)){ + vali=targetmat[[i]]+1; + if(i==1){ + plot(1:length(vali),vali,type='b',las=1,pch=20,main=paste('sgRNAs in',targetgene),ylab='Read counts',xlab='Samples',xlim=c(0.7,length(vali)+0.3),ylim = yrange,col=colors[(i %% length(colors))],xaxt='n',log='y') + axis(1,at=1:length(vali),labels=(collabel),las=2) + # lines(0:100,rep(1,101),col='black'); + }else{ + lines(1:length(vali),vali,type='b',pch=20,col=colors[(i %% length(colors))]) + } +} + + + +par(mfrow=c(1,1)); +@ +%__INDIVIDUAL_PAGE__ + + + + + + + + + +\end{document} + diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/test1.fastq.gz Binary file test-data/test1.fastq.gz has changed diff -r 5e2a28bee02d -r 81bbbddcf285 test-data/test2.fastq.gz Binary file test-data/test2.fastq.gz has changed