Package: ChIPexoQual 1.31.0

Rene Welch

ChIPexoQual: ChIPexoQual

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

Authors:Rene Welch, Dongjun Chung, Sunduz Keles

ChIPexoQual_1.31.0.tar.gz
ChIPexoQual_1.31.0.zip(r-4.5)ChIPexoQual_1.31.0.zip(r-4.4)ChIPexoQual_1.31.0.zip(r-4.3)
ChIPexoQual_1.31.0.tgz(r-4.4-any)ChIPexoQual_1.31.0.tgz(r-4.3-any)
ChIPexoQual_1.31.0.tar.gz(r-4.5-noble)ChIPexoQual_1.31.0.tar.gz(r-4.4-noble)
ChIPexoQual_1.31.0.tgz(r-4.4-emscripten)ChIPexoQual_1.31.0.tgz(r-4.3-emscripten)
ChIPexoQual.pdf |ChIPexoQual.html
ChIPexoQual/json (API)
NEWS

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

Peer review:

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-1.31.0(bioc 3.21)ChIPexoQual-1.30.0(bioc 3.20)

chipseqsequencingtranscriptionvisualizationqualitycontrolcoveragealignment

4.30 score 1 stars 5 scripts 329 downloads 1 mentions 14 exports 133 dependencies

Last updated 23 days agofrom:7b885836a3. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

Exports:ARCvURCplotbeta1beta2calculateParamDistExoDataExoDataBlacklistExoDataSubsamplingformatRegionsFSRDistplotMAplotnreadsparamDistparamDistBoxplotregionCompplot

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbiovizBasebitbit64bitopsblobbroomBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdplyrensembldbevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehexbinhighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngProtGenericspurrrR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryamlzlibbioc

ChIPexoQual: A quality control pipeline for ChIP-exo/nexus data.

Rendered fromvignette.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2018-01-24
Started: 2016-07-18