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ChIPseqR

Identifying Protein Binding Sites in High-Throughput Sequencing Data


Bioconductor version: Release (3.18)

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 (from within R, enter citation("ChIPseqR")):

Installation

To install this package, start R (version "4.3") 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 PDF R Script
Reference Manual PDF

Details

biocViews ChIPSeq, Infrastructure, Software
Version 1.56.0
In Bioconductor since BioC 2.5 (R-2.10) (14.5 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_1.56.0.tar.gz
Windows Binary ChIPseqR_1.56.0.zip
macOS Binary (x86_64) ChIPseqR_1.56.0.tgz
macOS Binary (arm64) ChIPseqR_1.56.0.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/
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