CexoR
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.13 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: 3.13
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 <pmadrigal at ebi.ac.uk>
citation("CexoR")):
Installation
To install this package, start R (version "4.1") 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
| Reference Manual |
Details
| biocViews | Genetics, Sequencing, Software, Transcription |
| Version | 1.30.1 |
| 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, knitr, rmarkdown |
| 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 | |
| Windows Binary | |
| macOS 10.13 (High Sierra) | |
| 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 | https://bioconductor.org/packages/CexoR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |