To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

MMDiff

Statistical Testing for ChIP-Seq data sets

Bioconductor version: 2.14

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>

Citation (from within R, enter citation("MMDiff")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("MMDiff")

 

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

Details

biocViews ChIPSeq, MultipleComparison, Software
Version 1.4.1
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 Archives

Follow Installation instructions to use this package in your R session.

Package Source MMDiff_1.4.1.tar.gz
Windows Binary MMDiff_1.4.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) MMDiff_1.4.1.tgz
Mac OS X 10.9 (Mavericks) MMDiff_1.4.1.tgz
Browse/checkout source (username/password: readonly)
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