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 (3.22)
Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.
Author: Pedro Madrigal [aut, cre]
Maintainer: Pedro Madrigal <pmadrigal at ebi.ac.uk>
citation("CexoR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | R Script | |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | ChIPSeq, Coverage, FunctionalGenomics, PeakDetection, Sequencing, Software |
| Version | 1.47.1 |
| In Bioconductor since | BioC 2.13 (R-3.0) (12 years) |
| License | Artistic-2.0 | GPL-2 + file LICENSE |
| Depends | R (>= 4.2.0), S4Vectors, IRanges |
| Imports | Rsamtools, Seqinfo, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation |
| System Requirements | |
| URL | https://github.com/pmb59/CexoR |
| Bug Reports | https://github.com/pmb59/CexoR/issues |
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 | CexoR_1.47.1.tar.gz |
| Windows Binary (x86_64) | CexoR_1.47.1.zip (64-bit only) |
| macOS Binary (x86_64) | CexoR_1.47.1.tgz |
| macOS Binary (arm64) | CexoR_1.47.1.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 |