dpeak

DOI: 10.18129/B9.bioc.dpeak    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see dpeak.

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

Bioconductor version: 3.13

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 "4.1") and enter:

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

BiocManager::install("dpeak")

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("dpeak")

 

PDF	R Script	dPeak
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, Genetics, Sequencing, Software, Transcription
Version	1.4.0
In Bioconductor since	BioC 3.11 (R-4.0) (1.5 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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	dpeak_1.4.0.tar.gz
Windows Binary	dpeak_1.4.0.zip
macOS 10.13 (High Sierra)	dpeak_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/dpeak
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dpeak
Package Short Url	https://bioconductor.org/packages/dpeak/
Package Downloads Report	Download Stats