MMDiff2

DOI: 10.18129/B9.bioc.MMDiff2  

Statistical Testing for ChIP-Seq data sets

Bioconductor version: Release (3.16)

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 (version "4.2") and enter:

if (!require("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 1.26.0
In Bioconductor since BioC 3.3 (R-3.3) (7 years)
License Artistic-2.0
Depends R (>= 3.5.0), 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_1.26.0.tar.gz
Windows Binary MMDiff2_1.26.0.zip
macOS Binary (x86_64) MMDiff2_1.26.0.tgz
macOS Binary (arm64) MMDiff2_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MMDiff2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MMDiff2
Bioc Package Browser https://code.bioconductor.org/browse/MMDiff2/
Package Short Url https://bioconductor.org/packages/MMDiff2/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: