Package: ChAMP 2.37.0

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:Yuan Tian [cre,aut], Tiffany Morris [ctb], Lee Stirling [ctb], Andrew Feber [ctb], Andrew Teschendorff [ctb], Ankur Chakravarthy [ctb]

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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'))

Peer review:

On BioConductor:ChAMP-2.37.0(bioc 3.21)ChAMP-2.36.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarraymethylationarraynormalizationtwochannelcopynumberdnamethylation

6.55 score 258 scripts 1.4k downloads 208 mentions 21 exports 253 dependencies

Last updated 2 months agofrom:bebfd7d521. Checks:OK: 1 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winWARNINGNov 19 2024
R-4.5-linuxWARNINGDec 19 2024
R-4.4-winWARNINGNov 19 2024
R-4.4-macWARNINGDec 19 2024

Exports:Block.GUIchamp.Blockchamp.CNAchamp.DMPchamp.DMRchamp.ebGSEAchamp.filterchamp.GSEAchamp.importchamp.imputechamp.loadchamp.normchamp.processchamp.QCchamp.refbasechamp.runCombatchamp.SVDCpG.GUIDMP.GUIDMR.GUIQC.GUI

Dependencies:abindaffyaffyioannotateAnnotationDbiAnnotationFilterAnnotationHubaskpassassortheadbackportsbase64base64encbeachmatbeanplotBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibbsseqbumphuntercachemChAMPdatacheckmateclicliprclueclustercodetoolscolorspacecombinatcommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirdendextenddichromatdigestDMRcateDNAcopydoParalleldoRNGdplyrDTedgeRensembldbevaluateExperimentHubfansifarverfastICAfastmapFDb.InfiniumMethylation.hg19filelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergeneLenDataBasegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2globaltestglueGO.dbgoseqgridExtragtablegtoolsGvizHDF5ArrayhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2Illumina450ProbeVariants.dbIlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestIlluminaHumanMethylationEPICanno.ilm10b4.hg19IlluminaHumanMethylationEPICmanifestIlluminaHumanMethylationEPICv2anno.20a1.hg38IlluminaHumanMethylationEPICv2manifestilluminaioimputeinterpIRangesisobandisvaiteratorsJADEjpegjquerylibjsonliteKEGGRESTKernSmoothknitrkpmtlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelimmalocfitlumimagrittrmarrayMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimissMethylmulttestmunsellnleqslvnlmennetnor1mixopensslorg.Hs.eg.dbpermutepillarpkgconfigplogrplotlyplyrpngpreprocessCoreprettydocprettyunitsprogresspromisesProtGenericspurrrquadprogqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsROCrpartRPMMRsamtoolsRSQLiterstudioapirtracklayerruvrvestS4ArraysS4VectorssassscalesscrimeselectrshinyshinythemessiggenessnowsourcetoolsSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselecttinytexTxDb.Hsapiens.UCSC.hg19.knownGenetxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwateRmelonwithrxfunXMLxml2xtableXVectoryamlzlibbioc

The Chip Analysis Methylation Pipeline

Yuan Tian, Tiffany J Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, and Andrew E Teschendorff

Rendered fromChAMP.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2020-09-08
Started: 2016-10-01

Readme and manuals

Help Manual

Help pageTopics
ChAMP-Chip Analysis Methylation PipelineChAMP-package ChAMP
Generate interactive plot for the result of champ.Block() function,Block.GUI
Identify Differential Methylation Blocks in Illumina HumanMethylation450 or HumanMethylationEPIC data.champ.Block
Inference of Copy Number Abberrations from intensity values.champ.CNA
Identify Differential Methylation Positions (DMP) and Numeric Covariate related CpGs in Illumina HumanMethylation450 or HumanMethylationEPIC data.champ.DMP
Applying Bumphunter, DMRcate or ProbeLasso Algorithms to detect Different Methylation Regions in a beta valued Methylation Dataset.champ.DMR
Empirical Bayes GSEA method.champ.ebGSEA
Do filtering on beta, M, intensity, Meth and UnMeth matrix.champ.filter
Do GSEA for DMP, DMR and other methylation data related results.champ.GSEA
Read data from IDAT file.champ.import
Conduct imputation for NA value on beta matrix and corresponding pd(Sample_sheet.csv) file.champ.impute
Upload of raw HumanMethylation450K or HumanMethylationEPIC data from IDAT files.champ.load
Normalization for HumanMethylation450 or HumanMethylationEPIC datachamp.norm
Process function to run all methods in ChAMP pipeline.champ.process
Plot quality control plot, mdsplot, densityPlot, dendrogram for a data set.champ.QC
Applying References-Base Methold to beta valued methylation data.champ.refbase
Function that uses ComBat to correct for batch effects. Multiple batch effect correction is allowed.champ.runCombat
Singular Value Decomposition analysis for batch effects prediciton in HumanMethylation450 or HumanMethylationEPIC datachamp.SVD
Generate interactive plot for summary information of a list of CpGsCpG.GUI
Generate interactive plot for the result of champ.DMP() function,DMP.GUI
Generate interactive plot for the result of champ.DMR() function,DMR.GUI
Generate interactive plot for Quality Control of a datasetQC.GUI