MMDiff2: Statistical Testing for ChIP-Seq data sets

This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).

AuthorGabriele Schweikert [cre, aut], David Kuo [aut]
Date of publicationNone
MaintainerGabriele Schweikert <gschweik@staffmail.ed.ac.uk>
LicenseArtistic-2.0
Version1.2.0

View on Bioconductor

Functions

Cfp1-Peaks Man page
compDists Man page
compHists Man page
compPvals Man page
Contrast Man page
Contrast,DBAmmd-method Man page
Counts Man page
Counts,DBAmmd-method Man page
DBAmmd Man page
DBAmmd-Accessors Man page
DBAmmd-class Man page
Dists Man page
Dists,DBAmmd-method Man page
estimateFragmentCenters Man page
Genome Man page
Genome,DBAmmd-method Man page
getPeakReads Man page
Hists Man page
Hists,DBAmmd-method Man page
metaData Man page
metaData,DBAmmd-method Man page
mm9-Genes Man page
MMD Man page
numPeaks Man page
numPeaks,DBAmmd-method Man page
numSamples Man page
numSamples,DBAmmd-method Man page
plotDists Man page
plotDISTS4Peak Man page
plotPeak Man page
Reads Man page
Reads,DBAmmd-method Man page
Regions Man page
Regions,DBAmmd-method Man page
reportResults Man page
runShinyMMDiff2 Man page
Samples Man page
Samples,DBAmmd-method Man page
server.MMDiff2 Man page
setContrast Man page
setContrast,DBAmmd-method Man page
setRegions Man page
setRegions,DBAmmd-method Man page
ui.MMDiff2 Man page

Files

MMDiff2/.BBSoptions
MMDiff2/DESCRIPTION
MMDiff2/NAMESPACE
MMDiff2/R
MMDiff2/R/AllGenerics.R MMDiff2/R/DBAmmd-Accessors.R MMDiff2/R/DBAmmd-Class.R MMDiff2/R/DBAmmd-Showmethods.R MMDiff2/R/DBAmmd-internal.R MMDiff2/R/MMDiff2_data.R MMDiff2/R/compDists.R MMDiff2/R/compHists.R MMDiff2/R/compPvals.R MMDiff2/R/createPeakMatrix.R MMDiff2/R/estimateFragmentCenters.R MMDiff2/R/getPeakReads.R MMDiff2/R/helperFcts.R MMDiff2/R/plotDISTS4Peak.R MMDiff2/R/plotDists.R MMDiff2/R/plotPeak.R MMDiff2/R/reportResults.R MMDiff2/R/runShinyMMDiff2.R MMDiff2/R/server.R MMDiff2/R/ui.R
MMDiff2/build
MMDiff2/build/vignette.rds
MMDiff2/data
MMDiff2/data/Cfp1-Peaks.RData
MMDiff2/data/MMD.RData
MMDiff2/data/datalist
MMDiff2/data/mm9-Genes.RData
MMDiff2/inst
MMDiff2/inst/doc
MMDiff2/inst/doc/MMDiff2.R
MMDiff2/inst/doc/MMDiff2.Rnw
MMDiff2/inst/doc/MMDiff2.pdf
MMDiff2/man
MMDiff2/man/Cfp1-Peaks.Rd MMDiff2/man/DBAmmd-Accessors.Rd MMDiff2/man/DBAmmd-class.Rd MMDiff2/man/MMD.Rd MMDiff2/man/compDists.Rd MMDiff2/man/compHists.Rd MMDiff2/man/compPvals.Rd MMDiff2/man/estimateFragmentCenters.Rd MMDiff2/man/getPeakReads.Rd MMDiff2/man/mm9-Genes.Rd MMDiff2/man/myGeneric.Rd MMDiff2/man/plotDISTS4Peak.Rd MMDiff2/man/plotDists.Rd MMDiff2/man/plotPeak.Rd MMDiff2/man/reportResults.Rd MMDiff2/man/runShinyMMDiff2.Rd MMDiff2/man/server.MMDiff2.Rd MMDiff2/man/ui.MMDiff2.Rd
MMDiff2/vignettes
MMDiff2/vignettes/MMDiff2-concordance.tex
MMDiff2/vignettes/MMDiff2.Rnw
MMDiff2/vignettes/ShinyMMDiff2Demo.png
MMDiff2/vignettes/framed.sty

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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