dpeak

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see dpeak.

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

Bioconductor version: 3.16

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, Genetics, Sequencing, Software, Transcription

Version 1.10.0

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

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_1.10.0.tar.gz

Windows Binary dpeak_1.10.0.zip (64-bit only)

macOS Binary (x86_64) dpeak_1.10.0.tgz

macOS Binary (arm64) dpeak_1.10.0.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 3.16 Source Archive