CexoR

This package is for version 3.12 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: 3.12

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 (IDR) 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 "4.0") 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

Details

biocViews Genetics, Sequencing, Software, Transcription
Version 1.28.0
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
Suggests RUnit, BiocGenerics, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package CexoR_1.28.0.tar.gz
Windows Binary CexoR_1.28.0.zip
macOS 10.13 (High Sierra) CexoR_1.28.0.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 3.12 Source Archive