DChIPRep

This package is for version 3.10 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: 3.10

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 "3.6") 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 1.16.0
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
Linking To
Enhances
Depends On Me
Imports Me
Suggests 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_1.16.0.tar.gz
Windows Binary DChIPRep_1.16.0.zip
Mac OS X 10.11 (El Capitan) DChIPRep_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DChIPRep
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DChIPRep
Bioc Package Browser https://code.bioconductor.org/browse/DChIPRep/
Package Short Url https://bioconductor.org/packages/DChIPRep/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive