dpeak

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)


Bioconductor version: Release (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")

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 1.16.0
In Bioconductor since BioC 3.11 (R-4.0) (4.5 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
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Package Archives

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

Source Package
Windows Binary dpeak_1.16.0.zip
macOS Binary (x86_64) dpeak_1.16.0.tgz
macOS Binary (arm64) dpeak_1.16.0.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/
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