CexoR

DOI: 10.18129/B9.bioc.CexoR  

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

Bioconductor version: Release (3.16)

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.

Author: Pedro Madrigal [aut, cre]

Maintainer: Pedro Madrigal <pmadrigal at ebi.ac.uk>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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	ChIPSeq, Coverage, FunctionalGenomics, PeakDetection, Sequencing, Software
Version	1.36.0
In Bioconductor since	BioC 2.13 (R-3.0) (9.5 years)
License	Artistic-2.0 | GPL-2 + file LICENSE
Depends	R (>= 4.2.0), S4Vectors, IRanges
Imports	Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation
LinkingTo
Suggests	RUnit, BiocGenerics, 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	CexoR_1.36.0.tar.gz
Windows Binary	CexoR_1.36.0.zip
macOS Binary (x86_64)	CexoR_1.36.0.tgz
macOS Binary (arm64)	CexoR_1.36.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CexoR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CexoR
Bioc Package Browser	https://code.bioconductor.org/browse/CexoR/
Package Short Url	https://bioconductor.org/packages/CexoR/
Package Downloads Report	Download Stats