DChIPRep

DOI: 10.18129/B9.bioc.DChIPRep    

DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

Bioconductor version: Release (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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DChIPRep")

Documentation

HTML	R Script	DChIPRepVignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, Sequencing, Software, WholeGenome
Version	1.8.0
In Bioconductor since	BioC 3.2 (R-3.2) (2.5 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
LinkingTo
Suggests	mgcv, testthat, BiocStyle, knitr, rmarkdown
SystemRequirements	Python 2.7, HTSeq (>= 0.6.1), numpy, argparse, sys
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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
Package Short Url	http://bioconductor.org/packages/DChIPRep/
Package Downloads Report	Download Stats