CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

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. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. If GeneRfold and GeneR are installed (http://bioconductor.case.edu/bioconductor/2.8/bioc/html/GeneRfold.html, http://bioc.ism.ac.jp/packages/2.8/bioc/html/GeneR.html), then the minimum free energy and bracket notation of secondary structure of gRNA and gRNA backbone constant region will be included in the summary file. This package leverages Biostrings and BSgenome packages.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CRISPRseek")
AuthorLihua Julie Zhu, Benjamin R. Holmes, Herve Pages, Michael Lawrence, Isana Veksler-Lublinsky, Victor Ambros, Neil Aronin and Michael Brodsky
Bioconductor views CRISPR GeneRegulation SequenceMatching
Date of publicationNone
MaintainerLihua Julie Zhu <julie.zhu@umassmed.edu>
LicenseGPL (>= 2)
Version1.14.1

View on Bioconductor

Functions

annotateOffTargets Man page
buildFeatureVectorForScoring Man page
calculategRNAEfficiency Man page
compare2Sequences Man page
CRISPRseek Man page
CRISPRseek-package Man page
filtergRNAs Man page
filterOffTarget Man page
findgRNAs Man page
foldgRNAs Man page
getOfftargetScore Man page
isPatternUnique Man page
offTargetAnalysis Man page
searchHits Man page
searchHits2 Man page
translatePattern Man page
uniqueREs Man page
writeHits Man page
writeHits2 Man page

Files

DESCRIPTION
NAMESPACE
R
R/annotateOfftargets.R R/buildFeatureVectorForScoring.R R/buildFeatureVectorForScoring2.R R/calculategRNAEfficiency.R R/compare2Sequences.R R/filterOffTarget.R R/filtergRNAs.R R/findgRNAs.R R/foldgRNAs.R R/getOfftargetScore.R R/getOfftargetScore2.R R/getSeqFromBed.R R/isPatternUnique.R R/offTargetAnalysis.R R/searchHits.R R/searchHits2.R R/translatePattern.R R/uniqueREs.R R/writeHits.R R/writeHits2.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/CRISPRseek.R
inst/doc/CRISPRseek.Rnw
inst/doc/CRISPRseek.pdf
inst/extdata
inst/extdata/DoenchNBT2014.csv
inst/extdata/ForTestinguniqueREs.RData
inst/extdata/NEBenzymes.fa
inst/extdata/NatureBiot2016SuppTable19DoenchRoot.csv
inst/extdata/RIPK1stop.fa
inst/extdata/T2.fa
inst/extdata/T2plus100OffTargets.bed
inst/extdata/cpf1.fa
inst/extdata/gRNAProvidedSearch
inst/extdata/gRNAProvidedSearch/OfftargetAnalysis.xls
inst/extdata/gRNAProvidedSearch/REcutDetails.xls
inst/extdata/gRNAProvidedSearch/Summary.xls
inst/extdata/gRNAProvidedSearch/gRNAsCRISPRseek.bed
inst/extdata/gRNAProvidedSearchNOoffTarget
inst/extdata/gRNAProvidedSearchNOoffTarget/OfftargetAnalysis.xls
inst/extdata/gRNAProvidedSearchNOoffTarget/Summary.xls
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/OfftargetAnalysis.xls
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/REcutDetails.xls
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/Summary.xls
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/gRNAsCRISPRseek.bed
inst/extdata/hits.txt
inst/extdata/inputseq.fa
inst/extdata/pairedSearch
inst/extdata/pairedSearch/withRE
inst/extdata/pairedSearch/withRE/OfftargetAnalysis.xls
inst/extdata/pairedSearch/withRE/REcutDetails.xls
inst/extdata/pairedSearch/withRE/Summary.xls
inst/extdata/pairedSearch/withRE/pairedgRNAs.xls
inst/extdata/pairedSearch/withoutRE
inst/extdata/pairedSearch/withoutRE/OfftargetAnalysis.xls
inst/extdata/pairedSearch/withoutRE/REcutDetails.xls
inst/extdata/pairedSearch/withoutRE/Summary.xls
inst/extdata/pairedSearch/withoutRE/pairedgRNAs.xls
inst/extdata/recreateTestResults.R
inst/extdata/rs362331C.fa
inst/extdata/rs362331T.fa
inst/extdata/seqs2.5prime.RData
inst/extdata/seqs2.RData
inst/extdata/seqs2CFD.RData
inst/extdata/test.bed
inst/extdata/testHsap_GATA1_ex2_gRNA1.fa
inst/extdata/testMouse
inst/extdata/testMouse/NOTannotateExon
inst/extdata/testMouse/NOTannotateExon/OfftargetAnalysis.xls
inst/extdata/testMouse/NOTannotateExon/REcutDetails.xls
inst/extdata/testMouse/NOTannotateExon/RIPK1stopallgRNAs.fa
inst/extdata/testMouse/NOTannotateExon/Summary.xls
inst/extdata/testMouse/NOTannotateExon/mRIPK1stop.gbk
inst/extdata/testMouse/NOTannotateExon/pairedgRNAs.xls
inst/extdata/testMouse/NOorgAnn
inst/extdata/testMouse/NOorgAnn/OfftargetAnalysis.xls
inst/extdata/testMouse/NOorgAnn/REcutDetails.xls
inst/extdata/testMouse/NOorgAnn/RIPK1stopallgRNAs.fa
inst/extdata/testMouse/NOorgAnn/Summary.xls
inst/extdata/testMouse/NOorgAnn/mRIPK1stop.gbk
inst/extdata/testMouse/NOorgAnn/pairedgRNAs.xls
inst/extdata/testMouse/WithorgAnn
inst/extdata/testMouse/WithorgAnn/OfftargetAnalysis.xls
inst/extdata/testMouse/WithorgAnn/REcutDetails.xls
inst/extdata/testMouse/WithorgAnn/RIPK1stopallgRNAs.fa
inst/extdata/testMouse/WithorgAnn/Summary.xls
inst/extdata/testMouse/WithorgAnn/mRIPK1stop.gbk
inst/extdata/testMouse/WithorgAnn/pairedgRNAs.xls
inst/extdata/testspeed.fa
inst/extdata/tobi2.fa
inst/extdata/unPairedSearch
inst/extdata/unPairedSearch/withRE
inst/extdata/unPairedSearch/withRE/OfftargetAnalysis.xls
inst/extdata/unPairedSearch/withRE/REcutDetails.xls
inst/extdata/unPairedSearch/withRE/Summary.xls
inst/extdata/unPairedSearch/withRE/pairedgRNAs.xls
inst/extdata/unPairedSearch/withoutRE
inst/extdata/unPairedSearch/withoutRE/OfftargetAnalysis.xls
inst/extdata/unPairedSearch/withoutRE/REcutDetails.xls
inst/extdata/unPairedSearch/withoutRE/Summary.xls
inst/extdata/unPairedSearch/withoutRE/pairedgRNAs.xls
inst/unitTests
inst/unitTests/test_compare2Sequences.R inst/unitTests/test_gRNAprovidedCompare2Seqs.R inst/unitTests/test_gRNAprovidedNoPAM.R inst/unitTests/test_getOfftargetScore2.R inst/unitTests/test_mouse_orgAnn_annotateExon.R inst/unitTests/test_offTargetAnalysis.R
man
man/CRISPRseek-package.Rd man/annotateOffTargets.Rd man/buildFeatureVectorForScoring.Rd man/calculategRNAEfficiency.Rd man/compare2Sequences.Rd man/filterOffTarget.Rd man/filtergRNA.Rd man/findgRNAs.Rd man/foldgRNAs.Rd man/getOfftargetScore.Rd man/isPatternUnique.Rd man/offTargetAnalysis.Rd man/searchHits.Rd man/searchHits2.Rd man/translatePattern.Rd man/uniqueREs.Rd man/writeHits.Rd man/writeHits2.Rd
tests
tests/runTests.R
vignettes
vignettes/CRISPRseek.Rnw

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