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: Release (3.1)

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 1.8.0
In Bioconductor since BioC 2.12 (R-3.0) (2.5 years)
License Artistic-2.0
Depends R (>= 2.14.0), GenomicRanges, parallel, DiffBind, GMD, Rsamtools
Imports GenomicRanges, IRanges, Biobase
LinkingTo
Suggests MMDiffBamSubset
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me MMDiffBamSubset
Build Report  

Package Archives

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

Package Source MMDiff_1.8.0.tar.gz
Windows Binary MMDiff_1.8.0.zip
Mac OS X 10.6 (Snow Leopard) MMDiff_1.8.0.tgz
Mac OS X 10.9 (Mavericks) MMDiff_1.8.0.tgz
Subversion source (username/password: readonly)
GitHub source https://github.com/Bioconductor-mirror/MMDiff/tree/release-3.1
Package Short Url http://bioconductor.org/packages/MMDiff/
Package Downloads Report Download Stats

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