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MMDiff2

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

Statistical Testing for ChIP-Seq data sets


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
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

Details

biocViews ChIPSeq, DifferentialPeakCalling, Sequencing, Software
Version 1.31.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
See More
Suggests MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me MMDiffBamSubset
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Package Archives

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

Source Package MMDiff2_1.31.0.tar.gz
Windows Binary MMDiff2_1.31.0.zip (64-bit only)
macOS Binary (x86_64) MMDiff2_1.31.0.tgz
macOS Binary (arm64) MMDiff2_1.31.0.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