Package: CRISPRseek 1.45.0
Lihua Julie Zhu
CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
The package includes functions to find potential guide RNAs for the CRISPR editing system including Base Editors and the Prime Editor 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. The package also output indels and their frequencies for Cas9 targeted sites.
Authors:
CRISPRseek_1.45.0.tar.gz
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CRISPRseek.pdf |CRISPRseek.html✨
CRISPRseek/json (API)
NEWS
| # Install 'CRISPRseek' in R: |
| install.packages('CRISPRseek', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:CRISPRseek-1.45.0(bioc 3.20)CRISPRseek-1.44.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:d63723fd8a
Exports:annotateOffTargetsbuildFeatureVectorForScoringcalculategRNAEfficiencycompare2SequencesdeepCpf1filtergRNAsfilterOffTargetfindgRNAsgetOfftargetScoreisPatternUniqueoffTargetAnalysisoffTargetAnalysisWithoutBSgenomepredictRelativeFreqIndelssearchHitssearchHits2translatePatternuniqueREswriteHitswriteHits2
Dependencies:abindade4askpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeclicodetoolsconfigcpp11crayoncurldata.tableDelayedArraydplyrfansiformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehashherehttrIRangesjsonlitekeraslambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmimemltoolsnlmeopensslpillarpixmappkgconfigpngprocessxpsR6rappdirsRcppRcppArmadilloRcppTOMLRCurlrestfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrprojrootRsamtoolsrstudioapirtracklayerS4ArraysS4VectorssegmentedseqinrsnowspSparseArraySummarizedExperimentsystensorflowtfautographtfrunstibbletidyselectUCSC.utilsutf8vctrswhiskerwithrXMLXVectoryamlzeallotzlibbioc
