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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MMDiff2")
AuthorGabriele Schweikert [cre, aut], David Kuo [aut]
Bioconductor views ChIPSeq DifferentialPeakCalling Sequencing Software
Date of publicationNone
MaintainerGabriele Schweikert <gschweik@staffmail.ed.ac.uk>
LicenseArtistic-2.0
Version1.4.0

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

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

Please suggest features or report bugs with the GitHub issue tracker.

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