DChIPRep

DOI: 10.18129/B9.bioc.DChIPRep    

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

Bioconductor version: Release (3.8)

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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DChIPRep", version = "3.8")

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 1.12.0
In Bioconductor since BioC 3.2 (R-3.2) (3 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_1.12.0.tar.gz
Windows Binary DChIPRep_1.12.0.zip
Mac OS X 10.11 (El Capitan) DChIPRep_1.12.0.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 http://bioconductor.org/packages/DChIPRep/
Package Downloads Report Download Stats

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