Package: ChAMP 2.43.0

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]

ChAMP_2.43.0.tar.gz
ChAMP_2.43.0.zip(r-4.7)ChAMP_2.43.0.zip(r-4.6)ChAMP_2.43.0.zip(r-4.5)
ChAMP_2.43.0.tgz(r-4.6-any)ChAMP_2.43.0.tgz(r-4.5-any)
ChAMP_2.43.0.tar.gz(r-4.7-any)ChAMP_2.43.0.tar.gz(r-4.6-any)
ChAMP_2.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ChAMP/json (API)

# Install 'ChAMP' in R:

install.packages('ChAMP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:ChAMP-2.43.0(bioc 3.24)ChAMP-2.42.0(bioc 3.23)

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

microarray methylationarray normalization twochannel copynumber dnamethylation

7.33 score 1 packages 472 scripts 208 mentions 20 exports 255 dependencies

Last updated from:a44889888f. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	1413
linux-devel-x86_64	WARNING	1699
source / vignettes	OK	1642
linux-release-x86_64	WARNING	1587
macos-release-arm64	WARNING	1000
macos-oldrel-arm64	WARNING	994
windows-devel	WARNING	1414
windows-release	WARNING	1426
windows-oldrel	WARNING	1451
wasm-release	OK	1362

Exports:Block.GUI champ.Block champ.CNA champ.DMP champ.DMR champ.filter champ.GSEA champ.import champ.impute champ.load champ.norm champ.process champ.QC champ.refbase champ.runCombat champ.SVD CpG.GUI DMP.GUI DMR.GUI QC.GUI

Dependencies:abind affy affyio annotate AnnotationDbi AnnotationFilter AnnotationHub askpass assorthead backports base64 base64enc beachmat beanplot BH BiasedUrn Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib bsseq bumphunter cachem ChAMPdata checkmate cigarillo cli clipr clue cluster codetools colorspace combinat commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir dendextend dichromat digest dir.expiry DMRcate DNAcopy doParallel doRNG dplyr DT edgeR ensembldb evaluate ExperimentHub farver fastICA fastmap FDb.InfiniumMethylation.hg19 filelock fontawesome foreach foreign formatR Formula fs futile.logger futile.options genefilter geneLenDataBase generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 globaltest glue GO.db goseq gridExtra gtable gtools Gviz h5mread HDF5Array highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 Illumina450ProbeVariants.db IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICv2anno.20a1.hg38 IlluminaHumanMethylationEPICv2manifest illuminaio impute interp IRanges isoband isva iterators JADE jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle limma locfit lumi magrittr marray MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi missMethyl multtest nleqslv nlme nnet nor1mix openssl org.Hs.eg.db otel permute pillar pkgconfig plotly plyr png preprocessCore prettydoc prettyunits progress promises ProtGenerics purrr quadprog qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools ROC rpart RPMM Rsamtools RSQLite rstudioapi rtracklayer ruv rvest S4Arrays S4Vectors S7 sass scales scrime selectr Seqinfo shiny shinythemes siggenes snow sourcetools SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sva sys tibble tidyr tidyselect tinytex TxDb.Hsapiens.UCSC.hg19.knownGene txdbmaker tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom wateRmelon withr xfun XML xml2 xtable XVector yaml

The Chip Analysis Methylation Pipeline

Rendered fromChAMP.Rmdusingknitr::rmarkdown

Last update: 2025-09-23
Started: 2016-10-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ChAMP-Chip Analysis Methylation Pipeline	ChAMP-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
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 data	champ.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 data	champ.SVD
Generate interactive plot for summary information of a list of CpGs	CpG.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 dataset	QC.GUI