CexoR

This package is for version 3.14 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: 3.14

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 "4.1") 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")

CexoR Vignette PDF R Script

Reference Manual PDF

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, Coverage, FunctionalGenomics, PeakDetection, Sequencing, Software

Version 1.32.0

In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)

License Artistic-2.0 | GPL-2 + file LICENSE

Depends R (>= 4.0.0), S4Vectors, IRanges

Imports Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation

System Requirements

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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_1.32.0.tar.gz

Windows Binary CexoR_1.32.0.zip

macOS 10.13 (High Sierra) CexoR_1.32.0.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

Old Source Packages for BioC 3.14 Source Archive