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]

crisprViz_1.9.0.tar.gz
crisprViz_1.7.0.zip(r-4.5)crisprViz_1.7.0.zip(r-4.4)crisprViz_1.7.0.zip(r-4.3)
crisprViz_1.9.0.tgz(r-4.4-any)crisprViz_1.9.0.tgz(r-4.3-any)
crisprViz_1.9.0.tar.gz(r-4.5-noble)crisprViz_1.9.0.tar.gz(r-4.4-noble)
crisprViz_1.9.0.tgz(r-4.4-emscripten)crisprViz_1.9.0.tgz(r-4.3-emscripten)
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'))

Peer review:

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

6.16 score 6 stars 2 packages 6 scripts 190 downloads 2 exports 170 dependencies

Last updated 2 months agofrom:aa8d738120. Checks:OK: 3 NOTE: 3 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winERROROct 30 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.4-winNOTEOct 30 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKNov 29 2024

Exports:plotGuideSetplotMultipleGuideSets

Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassbackportsbase64encbasiliskbasilisk.utilsBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncrisprBasecrisprBowtiecrisprDesigncrisprScorecrisprScoreDatacurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdir.expirydplyrensembldbevaluateExperimentHubfansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizherehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrR6randomForestrappdirsRbowtieRColorBrewerRcppRcppEigenRcppTOMLRCurlreadrrestfulrreticulateRhtslibrjsonrlangrmarkdownrpartrprojrootRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc

Introduction to crisprViz

Luke Hoberecht

Rendered fromintro.Rmdusingknitr::rmarkdownon Nov 29 2024.

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