Package: ChIPexoQual 1.37.0

Rene Welch

ChIPexoQual: ChIPexoQual

Package with a quality control pipeline for ChIP-exo/nexus data.

Authors:Rene Welch, Dongjun Chung, Sunduz Keles

ChIPexoQual_1.37.0.tar.gz
ChIPexoQual_1.37.0.zip(r-4.7)ChIPexoQual_1.37.0.zip(r-4.6)ChIPexoQual_1.37.0.zip(r-4.5)
ChIPexoQual_1.37.0.tgz(r-4.6-any)ChIPexoQual_1.37.0.tgz(r-4.5-any)
ChIPexoQual_1.37.0.tar.gz(r-4.7-any)ChIPexoQual_1.37.0.tar.gz(r-4.6-any)
ChIPexoQual_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ChIPexoQual/json (API)

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

Bug tracker:https://github.com/welch16/chipexoqual/issues

Datasets:
  • blacklists - 'list' of 'GRanges' objects with the blacklists generated by the ENCODE and modENCODE projects.
  • exoExample - 'ExoData' results for FoxA1 ChIP-exo experiment

On BioConductor:ChIPexoQual-1.37.0(bioc 3.24)ChIPexoQual-1.36.0(bioc 3.23)

chipseqsequencingtranscriptionvisualizationqualitycontrolcoveragealignment

3.30 score 1 stars 6 scripts 1 mentions 14 exports 129 dependencies

Last updated from:bb08b3dece. Checks:8 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING221
linux-devel-x86_64WARNING500
source / vignettesERROR352
linux-release-x86_64WARNING544
macos-release-arm64WARNING285
macos-oldrel-arm64WARNING308
windows-develWARNING478
windows-releaseWARNING489
windows-oldrelWARNING487
wasm-releaseOK205

Exports:ARCvURCplotbeta1beta2calculateParamDistExoDataExoDataBlacklistExoDataSubsamplingformatRegionsFSRDistplotMAplotnreadsparamDistparamDistBoxplotregionCompplot

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbiovizBasebitbit64bitopsblobbroomBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdplyrensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehexbinhighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpillarpkgconfigpngProtGenericspurrrR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryaml