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

Files in this package

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

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