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CexoR

This is the development version of CexoR; for the stable release version, see CexoR.

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

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("CexoR")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
CexoR Vignette PDF R Script
Reference Manual PDF
LICENSE Text

Details

biocViews ChIPSeq, Coverage, FunctionalGenomics, PeakDetection, Sequencing, Software
Version 1.39.0
In Bioconductor since BioC 2.13 (R-3.0) (10 years)
License Artistic-2.0 | GPL-2 + file LICENSE
Depends R (>= 4.2.0), S4Vectors, IRanges
Imports Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation
Linking To
Suggests RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CexoR_1.39.0.tar.gz
Windows Binary CexoR_1.39.0.zip
macOS Binary (x86_64) CexoR_1.39.0.tgz
macOS Binary (arm64) CexoR_1.39.0.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/
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