This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MMDiff2.
Bioconductor version: 3.8
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")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MMDiff2")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MMDiff2")
R Script | An Introduction to the MMDiff2 method | |
Reference Manual |
biocViews | ChIPSeq, DifferentialPeakCalling, Sequencing, Software |
Version | 1.10.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (3 years) |
License | Artistic-2.0 |
Depends | R (>= 3.3), Rsamtools, Biobase |
Imports | GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods |
LinkingTo | |
Suggests | MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | MMDiffBamSubset |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | MMDiff2_1.10.0.tar.gz |
Windows Binary | MMDiff2_1.10.0.zip |
Mac OS X 10.11 (El Capitan) | MMDiff2_1.10.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/MMDiff2 |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MMDiff2 |
Package Short Url | http://bioconductor.org/packages/MMDiff2/ |
Package Downloads Report | Download Stats |
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