Package: ChIPexoQual 1.31.0
Rene Welch
ChIPexoQual: ChIPexoQual
Package with a quality control pipeline for ChIP-exo/nexus data.
Authors:
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')) |
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-1.31.0(bioc 3.21)ChIPexoQual-1.30.0(bioc 3.20)
chipseqsequencingtranscriptionvisualizationqualitycontrolcoveragealignment
Last updated 2 months agofrom:7b885836a3. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | OK | Dec 18 2024 |
| R-4.5-linux | OK | Dec 18 2024 |
| R-4.4-win | OK | Dec 18 2024 |
| R-4.4-mac | OK | Dec 18 2024 |
| R-4.3-win | OK | Dec 18 2024 |
| R-4.3-mac | OK | Dec 18 2024 |
Exports:ARCvURCplotbeta1beta2calculateParamDistExoDataExoDataBlacklistExoDataSubsamplingformatRegionsFSRDistplotMAplotnreadsparamDistparamDistBoxplotregionCompplot
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbiovizBasebitbit64bitopsblobbroomBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdplyrensembldbevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehexbinhighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngProtGenericspurrrR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryamlzlibbioc
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 |