dpeak
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see dpeak.
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
Bioconductor version: 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("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 |
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 | |
| 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 (x86_64) | 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/ |
| Package Downloads Report | Download Stats |