ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Bioconductor version: 3.23 · Package version: 2.42.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChAMP")Details
| Maintainer | Yuan Tian <champ450k@gmail.com> |
| Author | Yuan Tian [cre,aut], Tiffany Morris [ctb], Lee Stirling [ctb], Andrew Feber [ctb], Andrew Teschendorff [ctb], Ankur Chakravarthy [ctb] |
| License | GPL-3 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel |
| Package Short Url | https://bioconductor.org/packages/ChAMP/ |
Citation
From within R, enter citation("ChAMP"):
Yuan Tian. ChAMP: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC. doi:10.18129/B9.bioc.ChAMP, R package version 2.42.0, https://bioconductor.org/packages/ChAMP.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ChAMP_2.42.0.tar.gz |
| Windows binary (x86_64) | ChAMP_2.42.0.zip |
| macOS binary (arm64) | ChAMP_2.42.0.tgz |
| macOS binary (x86_64) | ChAMP_2.42.0.tgz |
Dependencies
Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest, DT, RPMM
Imports: prettydoc, Hmisc, globaltest, sva, illuminaio, rmarkdown, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, goseq, missMethyl, ggplot2, GenomicRanges, qvalue, isva, doParallel, bumphunter, quadprog, shiny, shinythemes, plotly (>= 4.5.6), RColorBrewer, dendextend, matrixStats, combinat
Reverse dependencies
Suggests Me (1): GeoTcgaData