nuCpos

DOI: 10.18129/B9.bioc.nuCpos  

An R package for prediction of nucleosome positions

Bioconductor version: Release (3.16)

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. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provide chemical-map-based prediction, users are strongly encouraged to use it for dHMM-based prediction.

Author: Hiroaki Kato, Takeshi Urano

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

Installation

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

if (!require("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	1.16.3
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 years)
License	GPL-2
Depends	R (>= 4.2.0)
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_1.16.3.tar.gz
Windows Binary	nuCpos_1.16.3.zip
macOS Binary (x86_64)	nuCpos_1.16.3.tgz
macOS Binary (arm64)	nuCpos_1.16.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/nuCpos
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/nuCpos
Bioc Package Browser	https://code.bioconductor.org/browse/nuCpos/
Package Short Url	https://bioconductor.org/packages/nuCpos/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive