dpeak

DOI: 10.18129/B9.bioc.dpeak    

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

Bioconductor version: Release (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 (!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 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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_1.0.0.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
Package Short Url https://bioconductor.org/packages/dpeak/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive

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