dpeak

DOI: 10.18129/B9.bioc.dpeak  

This is the development version of dpeak; for the stable release version, see dpeak.

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

Bioconductor version: Development (3.19)

dPeak is a statistical framework for the high resolution identification of protein-DNA interaction sites using PET and SET ChIP-Seq and ChIP-exo data. It provides computationally efficient and user friendly interface to process ChIP-seq and ChIP-exo data, implement exploratory analysis, fit dPeak model, and export list of predicted binding sites for downstream analysis.

Author: Dongjun Chung, Carter Allen

Maintainer: Dongjun Chung <dongjun.chung at gmail.com>

Installation

To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("dpeak")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	ChIPSeq, Genetics, Sequencing, Software, Transcription
Version	1.15.0
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 years)
License	GPL (>= 2)
Depends	R (>= 4.0.0), methods, stats, utils, graphics, Rcpp
Imports	MASS, IRanges, BSgenome, grDevices, parallel
LinkingTo	Rcpp
Suggests	BSgenome.Ecoli.NCBI.20080805
SystemRequirements	GNU make, meme, fimo
Enhances
URL
BugReports	https://github.com/dongjunchung/dpeak/issues
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Build Report

Package Archives

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

Source Package
Windows Binary	dpeak_1.15.0.zip
macOS Binary (x86_64)	dpeak_1.15.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/dpeak
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dpeak
Bioc Package Browser	https://code.bioconductor.org/browse/dpeak/
Package Short Url	https://bioconductor.org/packages/dpeak/
Package Downloads Report	Download Stats