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Bioconductor - CexoR (development version)

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 (3.22)

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] ORCID: 0000-0003-1959-8199

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

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

To install this package, start R (version "4.5") 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")
Details biocViews ChIPSeq, Coverage, FunctionalGenomics, PeakDetection, Sequencing, Software Version 1.47.0 In Bioconductor since BioC 2.13 (R-3.0) (11.5 years) License Artistic-2.0 | GPL-2 + file LICENSE Depends R (>= 4.2.0), S4Vectors, IRanges Imports Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation System Requirements URL https://github.com/pmb59/CexoR Bug Reports https://github.com/pmb59/CexoR/issues See More Package Archives

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

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