To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CexoR")
In most cases, you don't need to download the package archive at all.
CexoR
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An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
Bioconductor version: Release (3.5)
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 <pm12 at sanger.ac.uk>
Maintainer: Pedro Madrigal <pm12 at sanger.ac.uk>
Citation (from within R,
enter citation("CexoR")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CexoR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CexoR")
| R Script | CexoR Vignette | |
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | Genetics, Sequencing, Software, Transcription |
| Version | 1.14.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (4 years) |
| License | Artistic-2.0 | GPL-2 + file LICENSE |
| Depends | R (>= 2.10.0), S4Vectors, IRanges |
| Imports | Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, BiocStyle |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CexoR_1.14.0.tar.gz |
| Windows Binary | CexoR_1.14.0.zip |
| Mac OS X 10.11 (El Capitan) | CexoR_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CexoR |
| Package Short Url | http://bioconductor.org/packages/CexoR/ |
| Package Downloads Report | Download Stats |
Documentation »
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