Package: crisprViz 1.9.0

Jean-Philippe Fortin

crisprViz: Visualization Functions for CRISPR gRNAs

Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

Authors:Jean-Philippe Fortin [aut, cre], Luke Hoberecht [aut]

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crisprViz.pdf |crisprViz.html✨
crisprViz/json (API)
NEWS

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

Bug tracker:https://github.com/crisprverse/crisprviz/issues

Datasets:
  • cage - CAGE peak annotation from AnnotationHub
  • cas12aGuideSet - Example GuideSet targeting the human LTN1 gene.
  • cas9GuideSet - Example GuideSet targeting the human LTN1 gene.
  • dnase - DNase I hypersensitive site annotation from AnnotationHub
  • gpr21GeneModel - CompressedGRangesList describing the human GPR21 gene.
  • gpr21GuideSet - Example GuideSet targeting the human GPR21 gene.
  • krasGeneModel - CompressedGRangesList describing the human KRAS gene.
  • krasGuideSet - Example GuideSet targeting the human KRAS gene.
  • ltn1GeneModel - CompressedGRangesList describing the human LTN1 gene.
  • mmp7GeneModel - CompressedGRangesList describing the human MMP7 gene.
  • mmp7GuideSet - Example GuideSet targeting the human MMP7 gene.
  • repeats - Subset of repeat elements for hg38.

On BioConductor:crisprViz-1.9.0(bioc 3.21)crisprViz-1.8.0(bioc 3.20)

crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-analysiscrispr-designgrnagrna-sequencegrna-sequencessgrnasgrna-designvisualization

6.23 score 7 stars 2 packages 6 scripts 215 downloads 2 exports 169 dependencies

Last updated 4 months agofrom:aa8d738120. Checks:3 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winNOTEJan 28 2025
R-4.5-macNOTEJan 28 2025
R-4.5-linuxNOTEJan 28 2025
R-4.4-winNOTEJan 28 2025
R-4.4-macNOTEJan 28 2025
R-4.3-winOKJan 28 2025
R-4.3-macOKJan 28 2025

Exports:plotGuideSetplotMultipleGuideSets

Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassbackportsbase64encbasiliskbasilisk.utilsBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncrisprBasecrisprBowtiecrisprDesigncrisprScorecrisprScoreDatacurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdir.expirydplyrensembldbevaluateExperimentHubfansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizherehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrR6randomForestrappdirsRbowtieRColorBrewerRcppRcppEigenRcppTOMLRCurlreadrrestfulrreticulateRhtslibrjsonrlangrmarkdownrpartrprojrootRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2XVectoryaml

Introduction to crisprViz

Luke Hoberecht

Rendered fromintro.Rmdusingknitr::rmarkdownon Jan 28 2025.

Last update: 2022-10-17
Started: 2022-07-18