MMDiff2

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see MMDiff2.

Statistical Testing for ChIP-Seq data sets

Bioconductor version: 3.15

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")

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 1.24.0

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

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

Package Archives

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

Source Package MMDiff2_1.24.0.tar.gz

Windows Binary MMDiff2_1.24.0.zip

macOS Binary (x86_64) MMDiff2_1.24.0.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

Old Source Packages for BioC 3.15 Source Archive