MMDiff2

DOI: 10.18129/B9.bioc.MMDiff2    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MMDiff2.

Statistical Testing for ChIP-Seq data sets

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MMDiff2")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.16.0
In Bioconductor since	BioC 3.3 (R-3.3) (4.5 years)
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
Links To Me
Build Report

Package Archives

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

Source Package	MMDiff2_1.16.0.tar.gz
Windows Binary	MMDiff2_1.16.0.zip
macOS 10.13 (High Sierra)	MMDiff2_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MMDiff2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MMDiff2
Package Short Url	https://bioconductor.org/packages/MMDiff2/
Package Downloads Report	Download Stats