MMDiff2

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of MMDiff2; for the stable release version, see MMDiff2.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Statistical Testing for ChIP-Seq data sets

Bioconductor version: Development (3.24)

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")):

Gabriele Schweikert, David Kuo. MMDiff2: Statistical Testing for ChIP-Seq data sets. doi:10.18129/B9.bioc.MMDiff2, R package version 1.41.1, https://bioconductor.org/packages/MMDiff2.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

An Introduction to the MMDiff2 method	PDF	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, DifferentialPeakCalling, Sequencing, Software
Version	1.41.1
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 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
System Requirements
URL

Suggests	MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	MMDiffBamSubset
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	MMDiff2_1.41.1.tar.gz
Windows Binary (x86_64)	MMDiff2_1.41.1.zip (64-bit only)
macOS Binary (big-sur-x86_64)	MMDiff2_1.41.1.tgz
macOS Binary (sonoma-arm64)	MMDiff2_1.41.1.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