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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DChIPRep")
In most cases, you don't need to download the package archive at all.
DChIPRep
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DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
Bioconductor version: Release (3.4)
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("https://bioconductor.org/biocLite.R")
biocLite("DChIPRep")
Documentation
| HTML | R Script | DChIPRepVignette |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, Sequencing, Software |
| Version | 1.4.0 |
| 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_1.4.0.tar.gz |
| Windows Binary | DChIPRep_1.4.0.zip |
| Mac OS X 10.9 (Mavericks) | DChIPRep_1.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DChIPRep/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/DChIPRep/ |
| Package Downloads Report | Download Stats |
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