To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MMDiff")
In most cases, you don't need to download the package archive at all.
MMDiff
|
This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see MMDiff.
Statistical Testing for ChIP-Seq data sets
Bioconductor version: 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:
## try http:// if https:// URLs are not supported
source("https://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")
| R Script | Analysing ChIP-Seq data with the "MMDiff" package | |
| Reference Manual |
Details
| biocViews | ChIPSeq, MultipleComparison, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3 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) |
| Git source | https://github.com/Bioconductor-mirror/MMDiff/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/MMDiff/ |
| Package Downloads Report | Download Stats |
Documentation »
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