To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MMDiff2")

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

MMDiff2

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MMDiff2.

Statistical Testing for ChIP-Seq data sets

Bioconductor version: 3.4

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]

Maintainer: Gabriele Schweikert <gschweik at staffmail.ed.ac.uk>

Citation (from within R, enter citation("MMDiff2")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MMDiff2")

Documentation

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

browseVignettes("MMDiff2")
PDF R Script An Introduction to the MMDiff2 method
PDF Reference Manual

Details

biocViews ChIPSeq, DifferentialPeakCalling, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
License Artistic-2.0
Depends R (>= 3.3), Rsamtools, Biobase
Imports GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods
LinkingTo
Suggests MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9
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 MMDiff2_1.2.0.tar.gz
Windows Binary MMDiff2_1.2.0.zip
Mac OS X 10.9 (Mavericks) MMDiff2_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/MMDiff2/tree/release-3.4
Package Short Url http://bioconductor.org/packages/MMDiff2/
Package Downloads Report Download Stats

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