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Bioconductor - MMDiff2 (development version)

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 (3.22)

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 "4.5") 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 1.37.1 In Bioconductor since BioC 3.3 (R-3.3) (9 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 Package Archives

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

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