Package: ChAMP 2.35.0
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Yuan Tian
ChAMP: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.
Authors:
ChAMP_2.35.0.tar.gz
ChAMP_2.35.0.zip(r-4.5)ChAMP_2.35.0.zip(r-4.4)ChAMP_2.35.0.zip(r-4.3)
ChAMP_2.35.0.tgz(r-4.4-any)ChAMP_2.33.0.tgz(r-4.3-any)
ChAMP_2.35.0.tar.gz(r-4.5-noble)ChAMP_2.35.0.tar.gz(r-4.4-noble)
ChAMP_2.35.0.tgz(r-4.4-emscripten)ChAMP_2.35.0.tgz(r-4.3-emscripten)
ChAMP.pdf |ChAMP.html✨
ChAMP/json (API)
NEWS
# Install 'ChAMP' in R: |
install.packages('ChAMP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:ChAMP-2.35.0(bioc 3.20)ChAMP-2.34.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:b1a7d15af4
Exports:Block.GUIchamp.Blockchamp.CNAchamp.DMPchamp.DMRchamp.ebGSEAchamp.filterchamp.GSEAchamp.importchamp.imputechamp.loadchamp.normchamp.processchamp.QCchamp.refbasechamp.runCombatchamp.SVDCpG.GUIDMP.GUIDMR.GUIQC.GUI
Dependencies:abindaffyaffyioannotateAnnotationDbiAnnotationFilterAnnotationHubaskpassbackportsbase64base64encbeachmatbeanplotBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibbsseqbumphuntercachemChAMPdatacheckmateclicliprclueclustercodetoolscolorspacecombinatcommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirdendextenddichromatdigestDMRcateDNAcopydoParalleldoRNGdplyrDTedgeRensembldbevaluateExperimentHubfansifarverfastICAfastmapFDb.InfiniumMethylation.hg19filelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergeneLenDataBasegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2globaltestglueGO.dbgoseqgridExtragtablegtoolsGvizHDF5ArrayhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2Illumina450ProbeVariants.dbIlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestIlluminaHumanMethylationEPICanno.ilm10b4.hg19IlluminaHumanMethylationEPICmanifestIlluminaHumanMethylationEPICv2anno.20a1.hg38IlluminaHumanMethylationEPICv2manifestilluminaioimputeinterpIRangesisobandisvaiteratorsJADEjpegjquerylibjsonliteKEGGRESTKernSmoothknitrkpmtlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelimmalocfitlumimagrittrmarrayMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimissMethylmulttestmunsellnleqslvnlmennetnor1mixopensslorg.Hs.eg.dbpermutepillarpkgconfigplogrplotlyplyrpngpreprocessCoreprettydocprettyunitsprogresspromisesProtGenericspurrrquadprogqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsROCrpartRPMMRsamtoolsRSQLiterstudioapirtracklayerruvS4ArraysS4VectorssassscalesscrimeshinyshinythemessiggenessnowsourcetoolsSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselecttinytexTxDb.Hsapiens.UCSC.hg19.knownGenetxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwateRmelonwithrxfunXMLxml2xtableXVectoryamlzlibbioc