CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
Version 1.16.0

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.

Browse man pages Browse package API and functions Browse package files

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)
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CRISPRseek")

Man pages

annotateOffTargets: annotate off targets
buildFeatureVectorForScoring: Build feature vectors
calculategRNAEfficiency: Calculate gRNA Efficiency
compare2Sequences: Compare 2 input sequences/sequence sets for possible guide...
CRISPRseek-package: Design of target-specific guide RNAs (gRNAs) in CRISPR-Cas9,...
filtergRNA: Filter gRNAs
filterOffTarget: filter off targets and generate reports.
findgRNAs: Find potential gRNAs
foldgRNAs: Fold gRNAs with the gRNA backbone constant region
getOfftargetScore: Calculate score for each off target
isPatternUnique: Output whether the input patterns occurs only once in the...
offTargetAnalysis: Design of target-specific guide RNAs for CRISPR-Cas9 system...
searchHits: Search for off targets in a sequence as DNAString
searchHits2: Search for off targets
translatePattern: translate pattern from IUPAC Extended Genetic Alphabet to...
uniqueREs: Output restriction enzymes that recognize only the gRNA...
writeHits: Write the hits of sequence search from a sequence to a file
writeHits2: Write the hits of sequence search to a file

Functions

CRISPRseek Man page
CRISPRseek-package Man page
annotateOffTargets Man page Source code
buildFeatureVectorForScoring Man page Source code
buildFeatureVectorForScoring2 Source code
calculategRNAEfficiency Man page Source code
compare2Sequences Man page Source code
compute_pair_index Source code
compute_pair_index2 Source code
compute_pair_index3 Source code
filterOffTarget Man page Source code
filtergRNAs Man page Source code
findgRNAs Man page Source code
foldgRNAs Man page Source code
getOfftargetScore Man page Source code
getOfftargetScore2 Source code
getSeqFromBed Source code
getgRNA.cut.sites Source code
isPatternUnique Man page Source code
mismatches_as_IntegerList Source code Source code
offTargetAnalysis Man page Source code
preprocess_me2 Source code
searchHits Man page Source code
searchHits2 Man page Source code
searchHitsInOneSeq2 Source code
searchHitsInOneSeq3 Source code
translatePattern Man page Source code
uniqueREs Man page Source code
writeHits Man page Source code
writeHits2 Man page Source code

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
CRISPRseek documentation built on May 20, 2017, 9:16 p.m.