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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
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This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see MMDiff2.
Statistical Testing for ChIP-Seq data sets
Bioconductor version: 3.3
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")
| R Script | An Introduction to the MMDiff2 method | |
| Reference Manual |
Details
| biocViews | ChIPSeq, DifferentialPeakCalling, Sequencing, Software |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | MMDiff2_1.0.2.tar.gz |
| Windows Binary | MMDiff2_1.0.2.zip |
| Mac OS X 10.9 (Mavericks) | MMDiff2_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/MMDiff2/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/MMDiff2/ |
| Package Downloads Report | Download Stats |
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