dpeak
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see dpeak.
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
Bioconductor version: 3.12
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("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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, Genetics, Sequencing, Software, Transcription |
| Version | 1.2.0 |
| 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_1.2.0.tar.gz |
| Windows Binary | dpeak_1.2.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | dpeak_1.2.0.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 3.12 | Source Archive |