MMDiff2
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MMDiff2.
Statistical Testing for ChIP-Seq data sets
Bioconductor version: 3.11
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("MMDiff2")
):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
Reference Manual |
Details
biocViews | ChIPSeq, DifferentialPeakCalling, Sequencing, Software |
Version | 1.16.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
License | Artistic-2.0 |
Depends | R (>= 3.3), 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 |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | MMDiff2_1.16.0.tar.gz |
Windows Binary | MMDiff2_1.16.0.zip |
macOS 10.13 (High Sierra) | MMDiff2_1.16.0.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 3.11 | Source Archive |