DOI: 10.18129/B9.bioc.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 (3.9)

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")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("CexoR", version = "3.9")

For older versions of R, please refer to the appropriate Bioconductor release.


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PDF R Script CexoR Vignette
PDF   Reference Manual


biocViews Genetics, Sequencing, Software, Transcription
Version 1.21.0
In Bioconductor since BioC 2.13 (R-3.0) (5.5 years)
License Artistic-2.0 | GPL-2 + file LICENSE
Depends R (>= 2.10.0), S4Vectors, IRanges
Imports Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation
Suggests RUnit, BiocGenerics, BiocStyle
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package CexoR_1.21.0.tar.gz
Windows Binary CexoR_1.21.0.zip
Mac OS X 10.11 (El Capitan) CexoR_1.21.0.tgz
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 http://bioconductor.org/packages/CexoR/
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