ChIPseqR

DOI: 10.18129/B9.bioc.ChIPseqR  

Identifying Protein Binding Sites in High-Throughput Sequencing Data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	Introduction to ChIPseqR
PDF		Reference Manual

Details

biocViews	ChIPSeq, Infrastructure, Software
Version	1.52.0
In Bioconductor since	BioC 2.5 (R-2.10) (13.5 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
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ChIPseqR_1.52.0.tar.gz
Windows Binary	ChIPseqR_1.52.0.zip (64-bit only)
macOS Binary (x86_64)	ChIPseqR_1.52.0.tgz
macOS Binary (arm64)	ChIPseqR_1.52.0.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