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.

AuthorLihua Julie Zhu, Benjamin R. Holmes, Herve Pages, Michael Lawrence, Isana Veksler-Lublinsky, Victor Ambros, Neil Aronin and Michael Brodsky
Date of publicationNone
MaintainerLihua Julie Zhu <julie.zhu@umassmed.edu>
LicenseGPL (>= 2)
Version1.14.0

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

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

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