dpeak

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see dpeak.

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)


Bioconductor version: 3.11

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>

Citation (from within R, enter citation("dpeak")):

Installation

To install this package, start R (version "4.0") and enter:


if (!require("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")
dPeak PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Genetics, Sequencing, Software, Transcription
Version 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL (>= 2)
Depends R (>= 4.0.0), methods, stats, utils, graphics, Rcpp
Imports MASS, IRanges, BSgenome, grDevices, parallel
System Requirements GNU make, meme, fimo
URL
Bug Reports https://github.com/dongjunchung/dpeak/issues
See More
Suggests BSgenome.Ecoli.NCBI.20080805
Linking To Rcpp
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 dpeak_1.0.0.tar.gz
Windows Binary dpeak_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) dpeak_1.0.0.tgz
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
Old Source Packages for BioC 3.11 Source Archive