MMDiff

Statistical Testing for ChIP-Seq data sets

Bioconductor version: Development (3.0)

This package detects statistically significant difference 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

Maintainer: Gabriele Schweikert <G.Schweikert at ed.ac.uk>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("MMDiff")

To cite this package in a publication, start R and enter:

    citation("MMDiff")

Documentation

PDF R Script Analysing ChIP-Seq data with the "MMDiff" package
PDF   Reference Manual

Details

biocViews ChIPSeq, MultipleComparison, Software
Version 1.5.0
In Bioconductor since BioC 2.12 (R-3.0)
License Artistic-2.0
Depends R (>= 2.14.0), GenomicRanges, parallel, DiffBind, GMD, Rsamtools
Imports GenomicRanges, IRanges, Biobase
Suggests MMDiffBamSubset
System Requirements
URL
Depends On Me
Imports Me
Suggests Me MMDiffBamSubset

Package Downloads

Package Source MMDiff_1.5.0.tar.gz
Windows Binary MMDiff_1.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) MMDiff_1.5.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center