MMDiff2
Statistical Testing for ChIP-Seq data sets
Bioconductor version: Release (3.20)
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 "4.4") 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 | 1.34.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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
| 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_1.34.0.tar.gz |
| Windows Binary (x86_64) | MMDiff2_1.34.0.zip |
| macOS Binary (x86_64) | MMDiff2_1.34.0.tgz |
| macOS Binary (arm64) | MMDiff2_1.34.0.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 |