NuPoP

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see NuPoP.

An R package for nucleosome positioning prediction


Bioconductor version: 3.15

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 http://nucleosome.stats.northwestern.edu.

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")

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")
NuPoP HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Genetics, HiddenMarkovModel, NucleosomePositioning, Software, Visualization
Version 2.4.0
In Bioconductor since BioC 2.7 (R-2.12) (13.5 years)
License GPL-2
Depends R (>= 4.0)
Imports graphics, utils
System Requirements
URL
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Suggests knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me nuCpos
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Build Report Build Report

Package Archives

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

Source Package NuPoP_2.4.0.tar.gz
Windows Binary NuPoP_2.4.0.zip (64-bit only)
macOS Binary (x86_64) NuPoP_2.4.0.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
Old Source Packages for BioC 3.15 Source Archive