Package: multicrispr 1.15.0

Aditya Bhagwat

multicrispr: Multi-locus multi-purpose Crispr/Cas design

This package is for designing Crispr/Cas9 and Prime Editing experiments. It contains functions to (1) define and transform genomic targets, (2) find spacers (4) count offtarget (mis)matches, and (5) compute Doench2016/2014 targeting efficiency. Care has been taken for multicrispr to scale well towards large target sets, enabling the design of large Crispr/Cas9 libraries.

Authors:Aditya Bhagwat [aut, cre], Richie ´Cotton [aut], Rene Wiegandt [ctb], Mette Bentsen [ctb], Jens Preussner [ctb], Michael Lawrence [ctb], Hervé Pagès [ctb], Johannes Graumann [sad], Mario Looso [sad, rth]

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multicrispr.pdf |multicrispr.html✨
multicrispr/json (API)
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Bug tracker:https://github.com/loosolab/multicrispr/issues

On BioConductor:multicrispr-1.15.0(bioc 3.20)multicrispr-1.14.0(bioc 3.19)

bioconductor-package

29 exports 1.00 score 163 dependencies 2 mentions

Last updated 2 months agofrom:b15b9a0d71

Exports:add_genome_matchesadd_inverse_strandadd_seqadd_target_matchesbed_to_grangeschar_to_grangesdouble_flankdown_flankdt2grextendextend_for_peextend_pe_to_ggextract_matchrangesextract_subrangesfind_ggfind_primespacersfind_spacersgenefile_to_grangesgenes_to_grangesgr2dthas_been_indexedindex_genomeindex_targetsplot_intervalsplot_karyogramread_rangesscore_ontargetsup_flankwrite_ranges

Dependencies:abindade4AnnotationDbiAnnotationFilteraskpassbackportsbamsignalsbase64encbezierBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspaceconfigcpp11crayonCRISPRseekcurldata.tableDBIDelayedArraydichromatdigestdplyrensembldbevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehashherehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonlitekaryoploteRKEGGRESTkerasknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemltoolsmunsellnlmennetopensslpillarpixmappkgconfigplogrplyrangespngprocessxProtGenericspspurrrR6rappdirsRbowtieRColorBrewerRcppRcppArmadilloRcppTOMLRCurlregioneRrestfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartrprojrootRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessegmentedseqinrsnowspSparseArraystringistringrSummarizedExperimentsystensorflowtfautographtfrunstibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewhiskerwithrxfunXMLXVectoryamlzeallotzlibbioc