nuCpos

DOI: 10.18129/B9.bioc.nuCpos    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see nuCpos.

An R package for prediction of nucleosome positions

Bioconductor version: 3.13

nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. In nuCpos, a duration hidden Markov model is trained with a chemical map of nucleosomes either from budding yeast, fission yeast, or mouse embryonic stem cells. nuCpos outputs the Viterbi (most probable) path of nucleosome-linker states, predicted nucleosome occupancy scores and histone binding affinity (HBA) scores as NuPoP does. nuCpos can also calculate local and whole nucleosomal HBA scores for a given 147-bp sequence. Furthermore, effect of genetic alterations on nucleosome occupancy can be predicted with this package. The parental package NuPoP, which is based on an MNase-seq-based map of budding yeast nucleosomes, was developed by Ji-Ping Wang and Liqun Xi, licensed under GPL-2.

Author: Hiroaki Kato, Takeshi Urano

Maintainer: Hiroaki Kato <hkato at med.shimane-u.ac.jp>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("nuCpos")

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("nuCpos")

 

PDF	R Script	An R package for prediction of nucleosome positioning
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Epigenetics, Genetics, HiddenMarkovModel, ImmunoOncology, NucleosomePositioning, Software
Version	1.10.0
In Bioconductor since	BioC 3.8 (R-3.5) (3 years)
License	file LICENSE
Depends	R (>= 3.6)
Imports	graphics, methods
LinkingTo
Suggests	NuPoP, Biostrings, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	nuCpos_1.10.0.tar.gz
Windows Binary	nuCpos_1.10.0.zip
macOS 10.13 (High Sierra)	nuCpos_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/nuCpos
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/nuCpos
Package Short Url	https://bioconductor.org/packages/nuCpos/
Package Downloads Report	Download Stats