ChIPseqR

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ChIPseqR.

Identifying Protein Binding Sites in High-Throughput Sequencing Data

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, Infrastructure, Software

Version 1.48.0

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_1.48.0.tar.gz

Windows Binary ChIPseqR_1.48.0.zip (32- & 64-bit)

macOS 10.13 (High Sierra) ChIPseqR_1.48.0.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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Old Source Packages for BioC 3.14 Source Archive