CexoR

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Bioconductor version: Development (3.0)

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalized 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 <pm12 at sanger.ac.uk>

Maintainer: Pedro Madrigal <pm12 at sanger.ac.uk>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("CexoR")

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

Documentation

PDF R Script CexoR Vignette
PDF   Reference Manual
Text   LICENSE

Details

biocViews Genetics, Sequencing, Software, Transcription
Version 1.3.3
In Bioconductor since BioC 2.13 (R-3.0)
License Artistic-2.0 | GPL-2 + file LICENSE
Depends R (>= 2.10.0), S4Vectors, IRanges
Imports Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr
Suggests RUnit, BiocGenerics, BiocStyle
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source CexoR_1.3.3.tar.gz
Windows Binary CexoR_1.3.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) CexoR_1.3.3.tgz
Mac OS X 10.9 (Mavericks) CexoR_1.3.3.tgz
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