CexoR

DOI: 10.18129/B9.bioc.CexoR  

This package is for version 3.17 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: 3.17

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")

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 1.38.0
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
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_1.38.0.tar.gz
Windows Binary CexoR_1.38.0.zip (64-bit only)
macOS Binary (x86_64) CexoR_1.38.0.tgz
macOS Binary (arm64) CexoR_1.38.0.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

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