MMDiff2
This is thereleased version of MMDiff2; for the devel version, seeMMDiff2.
Statistical Testing for ChIP-Seq data sets
Bioconductor version: Release (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("MMDiff2")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("MMDiff2")For older versions of R, please refer to the appropriateBioconductor 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 | 1.38.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (9.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | MMDiff2_1.38.0.tar.gz |
| Windows Binary (x86_64) | MMDiff2_1.38.0.zip (64-bit only) |
| macOS Binary (x86_64) | MMDiff2_1.38.0.tgz |
| macOS Binary (arm64) | MMDiff2_1.38.0.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 |