This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
Bioconductor version: Release (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 (from within R,
enter citation("CexoR")
):
To install this package, start R (version "4.1") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("CexoR")
For older versions of R, please refer to the appropriate Bioconductor release.
Reference Manual |
biocViews | Genetics, Sequencing, Software, Transcription |
Version | 1.30.1 |
In Bioconductor since | BioC 2.13 (R-3.0) (8 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, knitr, rmarkdown |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
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 |
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