Package: multicrispr 1.23.0
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:
multicrispr_1.23.0.tar.gz
multicrispr_1.23.0.zip(r-4.7)multicrispr_1.23.0.zip(r-4.6)multicrispr_1.23.0.zip(r-4.5)
multicrispr_1.23.0.tgz(r-4.6-any)multicrispr_1.23.0.tgz(r-4.5-any)
multicrispr_1.23.0.tar.gz(r-4.7-any)multicrispr_1.23.0.tar.gz(r-4.6-any)
multicrispr_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
multicrispr/json (API)
NEWS
| # Install 'multicrispr' in R: |
| install.packages('multicrispr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bhagwataditya/multicrispr/issues
On BioConductor:multicrispr-1.23.0(bioc 3.24)multicrispr-1.22.0(bioc 3.23)
Last updated from:aabd0f0ef3. Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 375 | ||
| linux-devel-x86_64 | ERROR | 510 | ||
| source / vignettes | ERROR | 481 | ||
| linux-release-x86_64 | ERROR | 535 | ||
| macos-release-arm64 | ERROR | 374 | ||
| macos-oldrel-arm64 | ERROR | 303 | ||
| windows-devel | ERROR | 411 | ||
| windows-release | ERROR | 409 | ||
| windows-oldrel | ERROR | 381 | ||
| wasm-release | OK | 351 |
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:abindade4AnnotationDbiAnnotationFilteraskpassbackportsbamsignalsbase64encbezierBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcellrangercheckmatecigarilloclicliprclustercodetoolscolorspaceconfigcpp11crayonCRISPRseekcurldata.tableDBIDelayedArraydichromatdigestdir.expirydplyrensembldbevaluatefarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablegtoolshashhavenherehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonlitekaryoploteRKEGGRESTkerasknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemltoolsnlmennetopensslopenxlsxpillarpixmappkgconfigplyrangespngprettyunitsprocessxprogressProtGenericspspurrrR.methodsS3R.ooR.utilsR6rappdirsRbowtieRColorBrewerRcppRcppArmadilloRcppTOMLRCurlreadrreadxlregioneRrematchrestfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibriorjsonrlangrmarkdownrpartrprojrootRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalessegmentedSeqinfoseqinrsnowspSparseArraystringistringrSummarizedExperimentsystensorflowtfautographtfrunstibbletidyrtidyselecttinytextzdbUCSC.utilsutf8VariantAnnotationvctrsviridisLitevroomwhiskerwithrwritexlxfunXMLXVectoryamlzeallotzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add genome matches | add_genome_matches |
| Add inverse strand | add_inverse_strand |
| Add sequence to GRanges | add_seq |
| Add target matches | add_target_matches |
| Read bedfile into GRanges | bed_to_granges |
| Convert character vector into GRanges | char_to_granges |
| Double flank | double_flank |
| Extend ranges for prime editing | extend_for_pe |
| Extend prime editing target to find GG sites | extend_pe_to_gg |
| Extract matching subranges | extract_matchranges |
| Extract subranges | extract_subranges |
| Find GG | find_gg |
| Find prime editing spacers | find_primespacers |
| Find crispr spacers in targetranges | find_spacers |
| Convert geneids into GRanges | genefile_to_granges genes_to_granges |
| GRanges <-> data.table | dt2gr gr2dt |
| Has been indexed? | has_been_indexed |
| Index genome | index_genome |
| Index targets | index_targets |
| Interval plot GRanges | plot_intervals |
| Karyo/Interval Plot GRanges(List) | plot_karyogram |
| Add on-target efficiency scores | score_ontargets |
| Extend or Flank GRanges | down_flank extend up_flank |
| Write GRanges to file | read_ranges write_ranges |
