To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("DChIPRep")

In most cases, you don't need to download the package archive at all.

DChIPRep

 

   

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

Bioconductor version: Release (3.5)

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 (from within R, enter citation("DChIPRep")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("DChIPRep")

Documentation

HTML R Script DChIPRepVignette
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, Sequencing, Software
Version 1.6.1
In Bioconductor since BioC 3.2 (R-3.2) (1.5 years)
License MIT + file LICENCE
Depends R (>= 3.3), 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.

Package Source DChIPRep_1.6.1.tar.gz
Windows Binary DChIPRep_1.6.1.zip
Mac OS X 10.11 (El Capitan) DChIPRep_1.6.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/DChIPRep/tree/release-3.5
Package Short Url http://bioconductor.org/packages/DChIPRep/
Package Downloads Report Download Stats

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