# HG changeset patch # User alperkucukural # Date 1446517170 18000 # Node ID 41db874eced0629bd35577d705615227e3fc07a1 # Parent 60666225371c3c48dd47f49411ba919e483a6ea0 Deleted selected files diff -r 60666225371c -r 41db874eced0 CRISPRSeek/CRISPRSeek/.shed.yml --- a/CRISPRSeek/CRISPRSeek/.shed.yml Mon Nov 02 21:19:01 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -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 60666225371c -r 41db874eced0 CRISPRSeek/CRISPRSeek/compare2sequences.xml --- a/CRISPRSeek/CRISPRSeek/compare2sequences.xml Mon Nov 02 21:19:01 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,147 +0,0 @@ - - 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 60666225371c -r 41db874eced0 CRISPRSeek/CRISPRSeek/crisprseek_macros.xml --- a/CRISPRSeek/CRISPRSeek/crisprseek_macros.xml Mon Nov 02 21:19:01 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ - - - - R - CRISPRseek - - - - - 10.1371/journal.pone.0108424 - - - diff -r 60666225371c -r 41db874eced0 CRISPRSeek/CRISPRSeek/offtargetanalysis.xml --- a/CRISPRSeek/CRISPRSeek/offtargetanalysis.xml Mon Nov 02 21:19:01 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,162 +0,0 @@ - - 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 60666225371c -r 41db874eced0 CRISPRSeek/CRISPRSeek/tool_dependencies.xml --- a/CRISPRSeek/CRISPRSeek/tool_dependencies.xml Mon Nov 02 21:19:01 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ - - - - - - - - -