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.

AuthorYuan Tian [cre,aut], Tiffany Morris [ctb], Lee Stirling [ctb], Andrew Feber [ctb], Andrew Teschendorff [ctb], Ankur Chakravarthy [ctb]
Date of publicationNone
MaintainerYuan Tian <champ450k@gmail.com>
LicenseGPL-3
Version2.6.0

View on Bioconductor

Man pages

Block.GUI: Generate interactive plot for the result of champ.Block()...

champ.Block: Identify Differential Methylation Blocks in Illumina...

champ.CNA: Inference of Copy Number Abberrations from intensity values.

champ.DMP: Identify Differential Methylation Positions (DMP) in Illumina...

champ.DMR: Applying Bumphunter, DMRcate or ProbeLasso Algorithms to...

champ.EpiMod: champ.EpiMod() infer differential methylation interactome...

champ.filter: Do filtering on beta or M matrix. So that user who have no...

champ.GSEA: Do GSEA for DMP, DMR and other methylation data related...

champ.impute: Conduct imputation for NA value on beta matrix and...

champ.load: Upload of raw HumanMethylation450K or HumanMethylationEPIC...

champ.norm: Normalization for HumanMethylation450 or HumanMethylationEPIC...

ChAMP-package: ChAMP-Chip Analysis Methylation Pipeline

champ.process: Process function to run all methods in ChAMP pipeline.

champ.QC: Plot quality control plot, mdsplot, densityPlot, dendrogram...

champ.refbase: Applying References-Base Methold to beta valued methylation...

champ.reffree: Applying RefFreeEWAS Methold to beta valued methylation data.

champ.runCombat: Function that uses ComBat to correct for batch effects....

champ.SVD: Singular Value Decomposition analysis for batch effects...

CpG.GUI: Generate interactive plot for summary information of a list...

DMP.GUI: Generate interactive plot for the result of champ.DMP()...

DMR.GUI: Generate interactive plot for the result of champ.DMR()...

QC.GUI: Generate interactive plot for Quality Control of a dataset

Files in this package

ChAMP/DESCRIPTION
ChAMP/NAMESPACE
ChAMP/R
ChAMP/R/Block.GUI.R ChAMP/R/CheckBMIQ.R ChAMP/R/CpG.GUI.R ChAMP/R/DMP.GUI.R ChAMP/R/DMR.GUI.R ChAMP/R/DoPBC.R ChAMP/R/EstDimRMTv2.R ChAMP/R/QC.GUI.R ChAMP/R/champ.BMIQ.R ChAMP/R/champ.Block.R ChAMP/R/champ.CNA.R ChAMP/R/champ.ComBat.R ChAMP/R/champ.DMP.R ChAMP/R/champ.DMR.R ChAMP/R/champ.EpiMod.R ChAMP/R/champ.GSEA.R ChAMP/R/champ.QC.R ChAMP/R/champ.SVD.R ChAMP/R/champ.colname.R ChAMP/R/champ.filter.R ChAMP/R/champ.impute.R ChAMP/R/champ.load.R ChAMP/R/champ.norm.R ChAMP/R/champ.process.R ChAMP/R/champ.read.R ChAMP/R/champ.refbase.R ChAMP/R/champ.reffree.R ChAMP/R/champ.runCombat.R ChAMP/R/zzz.R
ChAMP/build
ChAMP/build/vignette.rds
ChAMP/inst
ChAMP/inst/CITATION
ChAMP/inst/NEWS.Rd
ChAMP/inst/doc
ChAMP/inst/doc/ChAMP.R
ChAMP/inst/doc/ChAMP.Rmd
ChAMP/inst/doc/ChAMP.html
ChAMP/inst/extdata
ChAMP/inst/extdata/CNAimage.jpg
ChAMP/inst/extdata/CNAtext.jpg
ChAMP/inst/extdata/DMR.jpg
ChAMP/inst/extdata/DMRdistributionplot.png
ChAMP/inst/extdata/DMRoutput.jpg
ChAMP/inst/extdata/MVP1.jpg
ChAMP/inst/extdata/MVP2.jpg
ChAMP/inst/extdata/MVP3.jpg
ChAMP/inst/extdata/SVDsummary.pdf
ChAMP/inst/extdata/checkBMIQ.jpg
ChAMP/inst/extdata/densityPlot.jpg
ChAMP/inst/extdata/failedProbes.jpg
ChAMP/inst/extdata/figure1.pdf
ChAMP/inst/extdata/lasso.jpg
ChAMP/inst/extdata/logo4.jpg
ChAMP/inst/extdata/mdsPlot.jpg
ChAMP/inst/extdata/probeFeatures.jpg
ChAMP/inst/extdata/radius.jpg
ChAMP/inst/extdata/rawSampleCluster.jpg
ChAMP/inst/extdata/sampleSheetexample.jpg
ChAMP/inst/extdata/studyInfo.jpg
ChAMP/inst/extdata/studyInfo.png
ChAMP/inst/extdata/type1fit.jpg
ChAMP/inst/extdata/type2fit.jpg
ChAMP/man
ChAMP/man/Block.GUI.Rd ChAMP/man/ChAMP-package.Rd ChAMP/man/CpG.GUI.Rd ChAMP/man/DMP.GUI.Rd ChAMP/man/DMR.GUI.Rd ChAMP/man/QC.GUI.Rd ChAMP/man/champ.Block.Rd ChAMP/man/champ.CNA.Rd ChAMP/man/champ.DMP.Rd ChAMP/man/champ.DMR.Rd ChAMP/man/champ.EpiMod.Rd ChAMP/man/champ.GSEA.Rd ChAMP/man/champ.QC.Rd ChAMP/man/champ.SVD.Rd ChAMP/man/champ.filter.Rd ChAMP/man/champ.impute.Rd ChAMP/man/champ.load.Rd ChAMP/man/champ.norm.Rd ChAMP/man/champ.process.Rd ChAMP/man/champ.refbase.Rd ChAMP/man/champ.reffree.Rd ChAMP/man/champ.runCombat.Rd
ChAMP/vignettes
ChAMP/vignettes/ChAMP.Rmd
ChAMP/vignettes/ChAMP.bib
ChAMP/vignettes/ChAMP.css
ChAMP/vignettes/Figure
ChAMP/vignettes/Figure/BMIQ.jpg
ChAMP/vignettes/Figure/Block-1.png
ChAMP/vignettes/Figure/Block-2.png
ChAMP/vignettes/Figure/Block-3.png
ChAMP/vignettes/Figure/CNA.jpg
ChAMP/vignettes/Figure/CNAGroupPlot.jpg
ChAMP/vignettes/Figure/ChAMP_Pipeline.png
ChAMP/vignettes/Figure/CpGGUI.png
ChAMP/vignettes/Figure/DMP-1.png
ChAMP/vignettes/Figure/DMP-2.png
ChAMP/vignettes/Figure/DMP-3.png
ChAMP/vignettes/Figure/DMP-4.png
ChAMP/vignettes/Figure/DMP-5.png
ChAMP/vignettes/Figure/DMR-1.png
ChAMP/vignettes/Figure/DMR-2.png
ChAMP/vignettes/Figure/DMR-3.png
ChAMP/vignettes/Figure/DMR-4.png
ChAMP/vignettes/Figure/EpiMod.jpg
ChAMP/vignettes/Figure/Logo.jpg
ChAMP/vignettes/Figure/MVP-1.png
ChAMP/vignettes/Figure/MVP-2.png
ChAMP/vignettes/Figure/MVP-3.png
ChAMP/vignettes/Figure/MVP-4.png
ChAMP/vignettes/Figure/MVP-5.png
ChAMP/vignettes/Figure/QCGUI.jpg
ChAMP/vignettes/academic-medicine.csl
ChAMP/vignettes/header.html

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