ChIPseqR

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see ChIPseqR.

Identifying Protein Binding Sites in High-Throughput Sequencing Data


Bioconductor version: 3.17

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 1.54.0
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
System Requirements
URL
See More
Suggests
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 ChIPseqR_1.54.0.tar.gz
Windows Binary ChIPseqR_1.54.0.zip (64-bit only)
macOS Binary (x86_64) ChIPseqR_1.54.0.tgz
macOS Binary (arm64) ChIPseqR_1.54.0.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
Old Source Packages for BioC 3.17 Source Archive