CexoR
This is the released version of CexoR; for the devel version, see CexoR.
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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
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 | 1.50.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 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_1.50.0.tar.gz |
| Windows Binary (x86_64) | CexoR_1.50.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CexoR_1.50.0.tgz |
| macOS Binary (sonoma-arm64) | CexoR_1.50.0.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 |