DChIPRep
This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see DChIPRep.
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
Bioconductor version: 3.6
The DChIPRep package implements a methodology to assess differences between chromatin modification profiles in replicated ChIP-Seq studies as described in Chabbert et. al - http://www.dx.doi.org/10.15252/msb.20145776. A detailed description of the method is given in the software paper at https://doi.org/10.7717/peerj.1981
Author: Bernd Klaus [aut, cre], Christophe Chabbert [aut], Sebastian Gibb [ctb]
Maintainer: Bernd Klaus <bernd.klaus at embl.de>
citation("DChIPRep")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DChIPRep")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | ChIPSeq, Sequencing, Software, WholeGenome |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | MIT + file LICENCE |
| Depends | R (>= 3.4), DESeq2 |
| Imports | methods, stats, utils, ggplot2, fdrtool, reshape2, GenomicRanges, SummarizedExperiment, smoothmest, plyr, tidyr, assertthat, S4Vectors, purrr, soGGi, ChIPpeakAnno |
| System Requirements | Python 2.7, HTSeq (>= 0.6.1), numpy, argparse, sys |
| URL |
See More
| Suggests | mgcv, testthat, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DChIPRep_1.8.0.tar.gz |
| Windows Binary | DChIPRep_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | DChIPRep_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DChIPRep |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DChIPRep |
| Package Short Url | https://bioconductor.org/packages/DChIPRep/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |