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.

Author
Lihua Julie Zhu, Benjamin R. Holmes, Herve Pages, Michael Lawrence, Isana Veksler-Lublinsky, Victor Ambros, Neil Aronin and Michael Brodsky
Date of publication
None
Maintainer
Lihua Julie Zhu <julie.zhu@umassmed.edu>
License
GPL (>= 2)
Version
1.14.0

View on Bioconductor

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

Files in this package

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