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Bioconductor - CexoR

CexoR

This package is for version 3.10 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: 3.10

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

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

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

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

To install this package, start R (version "3.6") 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")
Details biocViews Genetics, Sequencing, Software, Transcription Version 1.24.0 In Bioconductor since BioC 2.13 (R-3.0) (10.5 years) License Artistic-2.0 | GPL-2 + file LICENSE Depends R (>= 2.10.0), S4Vectors, IRanges Imports Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation System Requirements URL See More Package Archives

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

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