Package: ChIPexoQual 1.37.0
Rene Welch
ChIPexoQual: ChIPexoQual
Package with a quality control pipeline for ChIP-exo/nexus data.
Authors:
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✨
card.svg |card.png
ChIPexoQual/json (API)
NEWS
| # 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
- 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
Last updated from:bb08b3dece. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 204 | ||
| linux-devel-x86_64 | OK | 463 | ||
| source / vignettes | OK | 395 | ||
| linux-release-x86_64 | OK | 454 | ||
| macos-release-arm64 | OK | 245 | ||
| macos-oldrel-arm64 | OK | 318 | ||
| windows-devel | OK | 476 | ||
| windows-release | OK | 482 | ||
| windows-oldrel | OK | 589 | ||
| wasm-release | OK | 186 |
Exports:ARCvURCplotbeta1beta2calculateParamDistExoDataExoDataBlacklistExoDataSubsamplingformatRegionsFSRDistplotMAplotnreadsparamDistparamDistBoxplotregionCompplot
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbiovizBasebitbit64bitopsblobbroomBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdplyrensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehexbinhighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpillarpkgconfigpngProtGenericspurrrR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ARCvURCplot | ARCvURCplot |
| beta1 methods | beta1 beta1,ExoData-method |
| beta2 methods | beta2 beta2,ExoData-method |
| 'list' of 'GRanges' objects with the blacklists generated by the ENCODE and modENCODE projects. | blacklists |
| calculateParamDist 'calculateParamDist' calculates the quality parameters of one iteration. This function samples 'nregions' rows from the stat matrix and fits the linear model 'lm(d ~ 0 + u + w)' | calculateParamDist |
| ExoData object and constructors | ExoData ExoData-class |
| ExoDataBlacklist | ExoDataBlacklist |
| ExoDataSubsampling | ExoDataSubsampling |
| 'ExoData' results for FoxA1 ChIP-exo experiment | exoExample |
| formatRegions 'formatRegions' separates the width, depth and uniquePos summary statistics from the 'ExoData' object to calculate the quality parameters/ | formatRegions |
| FSRDistplot | FSRDistplot |
| MAplot | MAplot |
| nreads methods | nreads nreads,ExoData-method |
| paramDist methods | paramDist paramDist,ExoData-method |
| paramDistBoxplot | paramDistBoxplot |
| regionCompplot | regionCompplot |