CexoR

DOI: 10.18129/B9.bioc.CexoR    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 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: 3.13

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 (IDR) for overlapping peak-pairs across biological replicates is estimated using the package 'idr'.

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

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

Installation

To install this package, start R (version "4.1") 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

PDF		Reference Manual

Details

biocViews	Genetics, Sequencing, Software, Transcription
Version	1.30.1
In Bioconductor since	BioC 2.13 (R-3.0) (8 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, knitr, rmarkdown
SystemRequirements
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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	https://bioconductor.org/packages/CexoR/
Package Downloads Report	Download Stats