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).

Author
Gabriele Schweikert [cre, aut], David Kuo [aut]
Date of publication
None
Maintainer
Gabriele Schweikert <gschweik@staffmail.ed.ac.uk>
License
Artistic-2.0
Version
1.2.0

View on Bioconductor

Man pages

Cfp1-Peaks
Peaks for Cfp1-data set
compDists
Compute distances between Peaks
compHists
Compute Peak histograms
compPvals
compute p-values
DBAmmd-Accessors
Extract data from DBAmmd objects
DBAmmd-class
Class DBAmmd
estimateFragmentCenters
estimate center of fragments
getPeakReads
Get reads from indexed bam files for defined regions
mm9-Genes
mm9-Genes
MMD
DBAmmd Object for Cfp1 example
myGeneric
Generics for DBAmmd-Class
plotDists
plotDists
plotDISTS4Peak
plotDISTS4Peak
plotPeak
plot Peak
reportResults
report results
runShinyMMDiff2
Shiny Application for interactive visualization of MMD,GMD...
server.MMDiff2
Shiny server code for interactive visualization of MMD...
ui.MMDiff2
ui component for interactive visualization of MMD,GMD and...

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