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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>

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

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

Reference Manual PDF

Details

biocViews ChIPSeq, Genetics, Sequencing, Software, Transcription
Version 1.15.0
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
Windows Binary dpeak_1.15.0.zip
macOS Binary (x86_64) dpeak_1.15.0.tgz
macOS Binary (arm64) dpeak_1.15.0.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