CexoR

DOI: 10.18129/B9.bioc.CexoR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see CexoR.

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Bioconductor version: 3.8

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package 'idr'.

Author: Pedro Madrigal <bioinformatics.engineer at gmail.com>

Maintainer: Pedro Madrigal <bioinformatics.engineer at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("CexoR")

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("CexoR")

 

PDF	R Script	CexoR Vignette
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Genetics, Sequencing, Software, Transcription
Version	1.20.0
In Bioconductor since	BioC 2.13 (R-3.0) (5.5 years)
License	Artistic-2.0 | GPL-2 + file LICENSE
Depends	R (>= 2.10.0), S4Vectors, IRanges
Imports	Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation
LinkingTo
Suggests	RUnit, BiocGenerics, BiocStyle
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	CexoR_1.20.0.tar.gz
Windows Binary	CexoR_1.20.0.zip
Mac OS X 10.11 (El Capitan)	CexoR_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CexoR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CexoR
Package Short Url	http://bioconductor.org/packages/CexoR/
Package Downloads Report	Download Stats