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comparison shm_downloads.htm @ 90:6809c63d9161 draft

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"planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
author rhpvorderman
date Tue, 25 Jan 2022 11:28:29 +0000
parents ba33b94637ca
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89:3c9d4d976c47 90:6809c63d9161
1 <html> 1 <html>
2 2
3 <head> 3 <head>
4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252"> 4 <meta http-equiv=Content-Type content="text/html; charset=UTF-8">
5 <meta name=Generator content="Microsoft Word 14 (filtered)"> 5 <meta name=Generator content="Microsoft Word 14 (filtered)">
6 <style> 6 <style>
7 <!-- 7 <!--
8 /* Font Definitions */ 8 /* Font Definitions */
9 @font-face 9 @font-face
75 75
76 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 76 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
77 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The SHM Overview 77 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The SHM Overview
78 table as a dataset:</span></u><span lang=EN-GB style='font-size:12.0pt; 78 table as a dataset:</span></u><span lang=EN-GB style='font-size:12.0pt;
79 font-family:"Times New Roman","serif"'> Allows downloading of the SHM Overview 79 font-family:"Times New Roman","serif"'> Allows downloading of the SHM Overview
80 table as a data set.  </span></p> 80 table as a data set.  </span></p>
81 81
82 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 82 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
83 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Motif data per 83 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Motif data per
84 sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family: 84 sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
85 "Times New Roman","serif"'> Provides a file that contains information for each 85 "Times New Roman","serif"'> Provides a file that contains information for each
95 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 95 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
96 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Base count for 96 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Base count for
97 every sequence:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family: 97 every sequence:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
98 "Times New Roman","serif"'> links to a page showing for each transcript the 98 "Times New Roman","serif"'> links to a page showing for each transcript the
99 sequence of the analysed region (as dependent on the sequence starts at filter), 99 sequence of the analysed region (as dependent on the sequence starts at filter),
100 the assigned subclass and the number of sequenced A,C,G and T’s.</span></p> 100 the assigned subclass and the number of sequenced A,C,G and T’s.</span></p>
101 101
102 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 102 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
103 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to 103 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
104 generate the percentage of mutations in AID and pol eta motives plot:</span></u><span 104 generate the percentage of mutations in AID and pol eta motives plot:</span></u><span
105 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> 105 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
133 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 133 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
134 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to 134 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
135 generate the frequency by class plot:</span></u><span lang=EN-GB 135 generate the frequency by class plot:</span></u><span lang=EN-GB
136 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Allows 136 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Allows
137 downloading the data used to generate frequency by class plot included in the 137 downloading the data used to generate frequency by class plot included in the
138 SHM frequency tab.           </span></p> 138 SHM frequency tab.           </span></p>
139 139
140 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 140 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
141 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for 141 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for
142 frequency by subclass:</span></u><span lang=EN-GB style='font-size:12.0pt; 142 frequency by subclass:</span></u><span lang=EN-GB style='font-size:12.0pt;
143 font-family:"Times New Roman","serif"'> Provides information of the number and 143 font-family:"Times New Roman","serif"'> Provides information of the number and
144 percentage of sequences that have 0%, 0-2%, 2-5%, 5-10%, 10-15%, 15-20%, 144 percentage of sequences that have 0%, 0-2%, 2-5%, 5-10%, 10-15%, 15-20%,
145 &gt;20% SHM. Information is provided for each subclass.</span></p> 145 &gt;20% SHM. Information is provided for each subclass.</span></p>
146 146
147 <p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB 147 <p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB
148 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> </span></p> 148 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> </span></p>
149 149
150 <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB 150 <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
151 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Transition 151 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Transition
152 Tables</span></b></p> 152 Tables</span></b></p>
153 153
265 the antigen selection tab.</span></p> 265 the antigen selection tab.</span></p>
266 266
267 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 267 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
268 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to 268 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
269 generate the aa mutation frequency plot for IGE:</span></u><span lang=EN-GB 269 generate the aa mutation frequency plot for IGE:</span></u><span lang=EN-GB
270 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>  Provides the 270 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>  Provides the
271 data used to generate the aa mutation frequency plot for all IGE sequences in 271 data used to generate the aa mutation frequency plot for all IGE sequences in
272 the antigen selection tab.</span></p> 272 the antigen selection tab.</span></p>
273 273
274 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 274 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
275 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline PDF (</span></u><span 275 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline PDF (</span></u><span
312 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 312 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
313 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGG 313 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGG
314 data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> 314 data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
315 Table output of the BASELINe analysis. Calculation of antigen selection as 315 Table output of the BASELINe analysis. Calculation of antigen selection as
316 performed by BASELINe are shown for each individual IGG sequence and the sum of 316 performed by BASELINe are shown for each individual IGG sequence and the sum of
317 all IGG sequences.        </span></p> 317 all IGG sequences.        </span></p>
318 318
319 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 319 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
320 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGM PDF:</span></u><span 320 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGM PDF:</span></u><span
321 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> PDF 321 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> PDF
322 containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family: 322 containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
371 371
372 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 372 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
373 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Sequence overlap 373 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Sequence overlap
374 between subclasses:</span></u><span lang=EN-GB style='font-size:12.0pt; 374 between subclasses:</span></u><span lang=EN-GB style='font-size:12.0pt;
375 font-family:"Times New Roman","serif"'> Link to the overlap table as provided 375 font-family:"Times New Roman","serif"'> Link to the overlap table as provided
376 under the clonality overlap tab.         </span></p> 376 under the clonality overlap tab.         </span></p>
377 377
378 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 378 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
379 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB 379 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
380 file with defined clones and subclass annotation:</span></u><span 380 file with defined clones and subclass annotation:</span></u><span
381 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> 381 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
386 386
387 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 387 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
388 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB 388 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
389 defined clones summary file:</span></u><span lang=EN-GB style='font-size:12.0pt; 389 defined clones summary file:</span></u><span lang=EN-GB style='font-size:12.0pt;
390 font-family:"Times New Roman","serif"'> Gives a summary of the total number of 390 font-family:"Times New Roman","serif"'> Gives a summary of the total number of
391 clones in all sequences and their clone size.           </span></p> 391 clones in all sequences and their clone size.           </span></p>
392 392
393 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 393 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
394 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB 394 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
395 file with defined clones of IGA:</span></u><span lang=EN-GB style='font-size: 395 file with defined clones of IGA:</span></u><span lang=EN-GB style='font-size:
396 12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the 396 12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the
421 of the total number of clones in all IGG sequences and their clone size.</span></p> 421 of the total number of clones in all IGG sequences and their clone size.</span></p>
422 422
423 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB 423 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
424 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB 424 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
425 file with defined clones of IGM:</span></u><span lang=EN-GB style='font-size: 425 file with defined clones of IGM:</span></u><span lang=EN-GB style='font-size:
426 12.0pt;font-family:"Times New Roman","serif"'> Downloads a table 426 12.0pt;font-family:"Times New Roman","serif"'> Downloads a table
427 with the calculation of clonal relation between all IGM sequences. For each 427 with the calculation of clonal relation between all IGM sequences. For each
428 individual transcript the results of the clonal assignment as provided by 428 individual transcript the results of the clonal assignment as provided by
429 Change-O are provided. Sequences with the same number in the CLONE column are 429 Change-O are provided. Sequences with the same number in the CLONE column are
430 considered clonally related. </span></p> 430 considered clonally related. </span></p>
431 431