# HG changeset patch # User alperkucukural # Date 1446563534 18000 # Node ID 891408eaa9f0ad8a65e9948d8243410b0af54249 # Parent 41db874eced0629bd35577d705615227e3fc07a1 Uploaded diff -r 41db874eced0 -r 891408eaa9f0 CRISPRSeek/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CRISPRSeek/.shed.yml Tue Nov 03 10:12:14 2015 -0500 @@ -0,0 +1,6 @@ +categories: [Sequence Analysis] +description: CRISPRseek Bioconductor package +homepage_url: http://www.bioconductor.org/packages/release/bioc/html/CRISPRseek.html +long_description: The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. +name: crisprseek +owner: nephantes diff -r 41db874eced0 -r 891408eaa9f0 CRISPRSeek/CRISPRSeek/test_data/inputfile.fa --- a/CRISPRSeek/CRISPRSeek/test_data/inputfile.fa Mon Nov 02 21:19:30 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ ->mRIPK1cds1_gR36f -AATGCAACCAGACATGTCCTTGG ->mRIPK1cds1_gR51f -GTCCTTGGACAATATTAAGATGG ->mRIPK1cds1_gR69f -GATGGCATCCAGTGACCTGCTGG ->mRIPK1cds1_gR91f -GAGAAGACAGACCTAGACAGCGG ->mRIPK1cds1_gR94f -AAGACAGACCTAGACAGCGGAGG ->mRIPK1cds1_gR100f -GACCTAGACAGCGGAGGCTTCGG ->mRIPK1cds1_gR101f -ACCTAGACAGCGGAGGCTTCGGG ->mRIPK1cds1_gR105f -AGACAGCGGAGGCTTCGGGAAGG ->mRIPK1cds1_gR133f -TTGTGTTACCACAGAAGCCATGG ->mRIPK1cds1_gR163f -ATCCTGAAAAAAGTATACACAGG ->mRIPK1cds1_gR164f -TCCTGAAAAAAGTATACACAGGG ->mRIPK1cds1_gR187f -CCCAACCGCGCTGAGTGAGTTGG ->mRIPK1cds1_gR188f -CCAACCGCGCTGAGTGAGTTGGG ->mRIPK1cds1_gR189f -CAACCGCGCTGAGTGAGTTGGGG ->mRIPK1cds1_gR190f -AACCGCGCTGAGTGAGTTGGGGG ->mRIPK1cds1_gR182r -TGCCCCCAACTCACTCAGCGCGG ->mRIPK1cds1_gR178r -CCCAACTCACTCAGCGCGGTTGG ->mRIPK1cds1_gR177r -CCAACTCACTCAGCGCGGTTGGG ->mRIPK1cds1_gR155r -GCCCTGTGTATACTTTTTTCAGG ->mRIPK1cds1_gR140r -TTTTCAGGATGACAAATCCATGG ->mRIPK1cds1_gR131r -TGACAAATCCATGGCTTCTGTGG ->mRIPK1cds1_gR121r -ATGGCTTCTGTGGTAACACAAGG ->mRIPK1cds1_gR92r -TCCCGAAGCCTCCGCTGTCTAGG ->mRIPK1cds1_gR74r -CTAGGTCTGTCTTCTCCAGCAGG ->mRIPK1cds1_gR67r -TGTCTTCTCCAGCAGGTCACTGG ->mRIPK1cds1_gR43r -TGCCATCTTAATATTGTCCAAGG ->mRIPK1cds1_gR33r -ATATTGTCCAAGGACATGTCTGG diff -r 41db874eced0 -r 891408eaa9f0 CRISPRSeek/compare2sequences.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CRISPRSeek/compare2sequences.xml Tue Nov 03 10:12:14 2015 -0500 @@ -0,0 +1,147 @@ + + CRISPRSeek compare2sequences + + crisprseek_macros.xml + + + + Rscript "${compare2sequences}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +The package includes functions to find potential guide RNAs for input target se- +quences, optionally filter guide RNAs without restriction enzyme cut site, or with- +out paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank se- +quence and indicate whether the target and off-targets are located in exon region or not. Poten- +tial guide RNAs are annotated with total score of the top5 and topN off-targets, de- +tailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. + +**Description** + +Generate all possible guide RNAs (gRNAs) for two input sequences, or two sets of sequences and generate scores for potential off-targets in the other sequence. + +**Usage** + + compare2Sequences(inputFile1Path, inputFile2Path, inputNames=c("Seq1", "Seq2"), format = "fasta", findgRNAsWithREcutOnly = FALSE, searchDirection=c("both","1to2", "2to1"), REpatternFile=system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek"), minREpatternSize = 6, overlap.gRNA.positions = c(17, 18), findPairedgRNAOnly = FALSE, min.gap = 0, max.gap = 20, gRNA.name.prefix = "gRNA", PAM.size = 3, gRNA.size = 20, PAM = "NGG", PAM.pattern = "N[A|G]G$", max.mismatch = 3, outputDir, weights = c(0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508, 0.613, 0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583), overwrite = FALSE) + +**Author(s)** + +Lihua Julie Zhu and Michael Brodsky Maintainer: julie.zhu@umassmed.edu + +Alper Kucukural, Galaxy Maintainer: alper.kucukural@umassmed.edu + +**Citation** + +(from within R, enter citation("CRISPRseek")): + +Zhu LJ, Holmes BR, Aronin N and Brodsky MH (2014). “CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems.” PLoS one, 9(9). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172692/. + +**References** + +Patrick D Hsu, David A Scott, Joshua A Weinstein, F Ann Ran, Silvana Konermann, Vineeta Agar- +wala, Yinqing Li, Eli J Fine, Xuebing Wu, Ophir Shalem, Thomas J Cradick, Luciano A Marraffini, +Gang Bao, Feng Zhang (2013) DNA targeting specificity of rNA-guided Cas9 nucleases. Nature +Biotechnology 31:827-83 + +Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM.CAS9 +transcriptional activators for target specificity screening and paired nickases for cooperative genome +engineering. Nat Biotechnol. 2013. 31(9):833-8 Patrick D Hsu, David A Scott, Joshua A Wein- +stein, F Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli J Fine, Xuebing Wu, +Ophir Shalem, Thomas J Cradick, Luciano A Marraffini, Gang Bao, Feng Zhang. DNA targeting +specificity of rNA-guided Cas9 nucleases. Nat Biotechnol. 2013. 31:827-834 + +**Reference Manual and Materials** + +http://www.bioconductor.org/packages/release/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.pdf + +http://www.bioconductor.org/packages/release/bioc/manuals/CRISPRseek/man/CRISPRseek.pdf + +http://www.bioconductor.org/packages/release/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.R + + + + + + + + + + diff -r 41db874eced0 -r 891408eaa9f0 CRISPRSeek/crisprseek_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CRISPRSeek/crisprseek_macros.xml Tue Nov 03 10:12:14 2015 -0500 @@ -0,0 +1,13 @@ + + + + R + CRISPRseek + + + + + 10.1371/journal.pone.0108424 + + + diff -r 41db874eced0 -r 891408eaa9f0 CRISPRSeek/offtargetanalysis.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CRISPRSeek/offtargetanalysis.xml Tue Nov 03 10:12:14 2015 -0500 @@ -0,0 +1,162 @@ + + CRISPRSeek offTargetAnalysis + + crisprseek_macros.xml + + + + Rscript "${offTargetAnalysis}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +The package includes functions to find potential guide RNAs for input target se- +quences, optionally filter guide RNAs without restriction enzyme cut site, or with- +out paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank se- +quence and indicate whether the target and off-targets are located in exon region or not. Poten- +tial guide RNAs are annotated with total score of the top5 and topN off-targets, de- +tailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. + +**Description** + +Design of target-specific gRNAs for the CRISPR-Cas9 system by automatically finding potential +gRNAs (paired/not paired), with/without restriction enzyme cut site(s) in a given sequence, search- +ing for off targets with user defined maximum number of mismatches, calculating score of each +off target based on mismatch positions in the off target and a penalty weight matrix, filtering off +targets with user-defined criteria, and annotating off targets with flank sequences, whether located +in exon or not. Summary report is also generated with gRNAs ranked by total topN off target +score, annotated with restriction enzyme cut sites and possible paired gRNAs. Detailed paired gR- +NAs information and restriction enzyme cut sites are stored in separate files in the output directory +specified by the user. In total, four tab delimited files are generated in the output directory: Off- +targetAnalysis.xls (off target details), Summary.xls (gRNA summary), REcutDetails.xls (restriction +enzyme cut sites of each gRNA), and pairedgRNAs.xls (potential paired gRNAs). + +**Author(s)** + +Lihua Julie Zhu and Michael Brodsky Maintainer: julie.zhu@umassmed.edu + +**Citation** + +(from within R, enter citation("CRISPRseek")): + +Zhu LJ, Holmes BR, Aronin N and Brodsky MH (2014). “CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems.” PLoS one, 9(9). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172692/. + +**References** + +http://bioconductor.org/packages/2.8/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf + +Patrick D Hsu, David A Scott, Joshua A Weinstein, F Ann Ran, Silvana Konermann, Vineeta Agar- +wala, Yinqing Li, Eli J Fine, Xuebing Wu, Ophir Shalem, Thomas J Cradick, Luciano A Marraffini, +Gang Bao, Feng Zhang (2013) DNA targeting specificity of rNA-guided Cas9 nucleases. Nature +Biotechnology 31:827-83 + +Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM.CAS9 +transcriptional activators for target specificity screening and paired nickases for cooperative genome +engineering. Nat Biotechnol. 2013. 31(9):833-8 Patrick D Hsu, David A Scott, Joshua A Wein- +stein, F Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli J Fine, Xuebing Wu, +Ophir Shalem, Thomas J Cradick, Luciano A Marraffini, Gang Bao, Feng Zhang. DNA targeting +specificity of rNA-guided Cas9 nucleases. Nat Biotechnol. 2013. 31:827-834 + +**Reference Manual and Materials** + +http://www.bioconductor.org/packages/release/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.pdf + +http://www.bioconductor.org/packages/release/bioc/manuals/CRISPRseek/man/CRISPRseek.pdf + +http://www.bioconductor.org/packages/release/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.R + + + + + + + + + + diff -r 41db874eced0 -r 891408eaa9f0 CRISPRSeek/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CRISPRSeek/tool_dependencies.xml Tue Nov 03 10:12:14 2015 -0500 @@ -0,0 +1,9 @@ + + + + + + + + +