DChIPRep

This package is for version 3.7 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: 3.7

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 (version "3.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DChIPRep")
DChIPRepVignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Sequencing, Software, WholeGenome
Version 1.10.0
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
URL
See More
Suggests mgcv, testthat, BiocStyle, knitr, rmarkdown
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Depends On Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DChIPRep_1.10.0.tar.gz
Windows Binary DChIPRep_1.10.0.zip
Mac OS X 10.11 (El Capitan) DChIPRep_1.10.0.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 3.7 Source Archive