NuPoP

DOI: 10.18129/B9.bioc.NuPoP  

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

An R package for nucleosome positioning prediction

Bioconductor version: 3.16

NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.

Author: Ji-Ping Wang <jzwang at northwestern.edu>; Liqun Xi <liqunxi02 at gmail.com>; Oscar Zarate <zarate at u.northwestern.edu>

Maintainer: Ji-Ping Wang<jzwang at northwestern.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("NuPoP")

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("NuPoP")

 

HTML	R Script	NuPoP
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Genetics, HiddenMarkovModel, NucleosomePositioning, Software, Visualization
Version	2.6.3
In Bioconductor since	BioC 2.7 (R-2.12) (12.5 years)
License	GPL-2
Depends	R (>= 4.0)
Imports	graphics, utils
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	nuCpos
Links To Me
Build Report

Package Archives

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

Source Package	NuPoP_2.6.3.tar.gz
Windows Binary	NuPoP_2.6.3.zip
macOS Binary (x86_64)	NuPoP_2.6.3.tgz
macOS Binary (arm64)	NuPoP_2.6.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NuPoP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NuPoP
Bioc Package Browser	https://code.bioconductor.org/browse/NuPoP/
Package Short Url	https://bioconductor.org/packages/NuPoP/
Package Downloads Report	Download Stats