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MMDiff2

Statistical Testing for ChIP-Seq data sets


Bioconductor version: Release (3.18)

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 "4.3") 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")
An Introduction to the MMDiff2 method PDF R Script
Reference Manual PDF

Details

biocViews ChIPSeq, DifferentialPeakCalling, Sequencing, Software
Version 1.30.0
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
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Suggests MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9
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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_1.30.0.tar.gz
Windows Binary MMDiff2_1.30.0.zip
macOS Binary (x86_64) MMDiff2_1.30.0.tgz
macOS Binary (arm64) MMDiff2_1.30.0.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