DChIPRep

DOI: 10.18129/B9.bioc.DChIPRep    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.11 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: 3.11

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 (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	DChIPRepVignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, Sequencing, Software, WholeGenome
Version	1.18.0
In Bioconductor since	BioC 3.2 (R-3.2) (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
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	DChIPRep_1.18.0.tar.gz
Windows Binary	DChIPRep_1.18.0.zip
macOS 10.13 (High Sierra)	DChIPRep_1.18.0.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