ChIPseqR
This is the released version of ChIPseqR; for the devel version, see ChIPseqR.
Identifying Protein Binding Sites in High-Throughput Sequencing Data
Bioconductor version: Release (3.23)
ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.
Author: Peter Humburg
Maintainer: Peter Humburg <peter.humburg at gmail.com>
citation("ChIPseqR")):
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("ChIPseqR")
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("ChIPseqR")| Introduction to ChIPseqR | R Script | |
| Reference Manual |
Details
| biocViews | ChIPSeq, Infrastructure, Software |
| Version | 1.66.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (17 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10.0), methods, BiocGenerics, S4Vectors(>= 0.9.25) |
| Imports | Biostrings, fBasics, GenomicRanges, IRanges(>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils |
| System Requirements | |
| URL |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChIPseqR_1.66.0.tar.gz |
| Windows Binary (x86_64) | ChIPseqR_1.66.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | ChIPseqR_1.66.0.tgz |
| macOS Binary (sonoma-arm64) | ChIPseqR_1.66.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ChIPseqR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChIPseqR |
| Bioc Package Browser | https://code.bioconductor.org/browse/ChIPseqR/ |
| Package Short Url | https://bioconductor.org/packages/ChIPseqR/ |
| Package Downloads Report | Download Stats |