Package: multicrispr 1.17.1

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]

multicrispr_1.17.1.tar.gz
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multicrispr_1.17.1.tgz(r-4.4-any)multicrispr_1.17.1.tgz(r-4.3-any)
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multicrispr.pdf |multicrispr.html✨
multicrispr/json (API)
NEWS

# Install 'multicrispr' in R:
install.packages('multicrispr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bhagwataditya/multicrispr/issues

On BioConductor:multicrispr-1.17.1(bioc 3.21)multicrispr-1.16.0(bioc 3.20)

crisprsoftware

5.65 score 2 scripts 175 downloads 2 mentions 29 exports 163 dependencies

Last updated 25 days agofrom:2519b98a8b. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winOKNov 29 2024
R-4.4-macOKNov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

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

Genome arithmetics

Aditya M Bhagwat

Rendered fromgenome_arithmetics.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2020-09-06
Started: 2020-07-21

Crispr/Cas9 gRNA design

Aditya M Bhagwat

Rendered fromcrispr_grna_design.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2021-12-23
Started: 2020-09-06

Prime Editing

Aditya M Bhagwat

Rendered fromprime_editing.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2020-09-06
Started: 2020-09-06

Readme and manuals

Help Manual

Help pageTopics
Add genome matchesadd_genome_matches
Add inverse strandadd_inverse_strand
Add sequence to GRangesadd_seq
Add target matchesadd_target_matches
Read bedfile into GRangesbed_to_granges
Convert character vector into GRangeschar_to_granges
Double flankdouble_flank
Extend ranges for prime editingextend_for_pe
Extend prime editing target to find GG sitesextend_pe_to_gg
Extract matching subrangesextract_matchranges
Extract subrangesextract_subranges
Find GGfind_gg
Find prime editing spacersfind_primespacers
Find crispr spacers in targetrangesfind_spacers
Convert geneids into GRangesgenefile_to_granges genes_to_granges
GRanges <-> data.tabledt2gr gr2dt
Has been indexed?has_been_indexed
Index genomeindex_genome
Index targetsindex_targets
Interval plot GRangesplot_intervals
Karyo/Interval Plot GRanges(List)plot_karyogram
Add on-target efficiency scoresscore_ontargets
Extend or Flank GRangesdown_flank extend up_flank
Write GRanges to fileread_ranges write_ranges