NuPoP

DOI: 10.18129/B9.bioc.NuPoP    

This is the development version of NuPoP; for the stable release version, see NuPoP.

An R package for nucleosome positioning prediction

Bioconductor version: Development (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>

Citation (from within R, enter citation("NuPoP")):

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.5.5
In Bioconductor since BioC 2.7 (R-2.12) (12 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_2.5.5.tar.gz
Windows Binary NuPoP_2.5.5.zip
macOS 10.13 (High Sierra) NuPoP_2.5.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/NuPoP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NuPoP
Package Short Url https://bioconductor.org/packages/NuPoP/
Package Downloads Report Download Stats

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