nuCpos

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see nuCpos.

An R package for prediction of nucleosome positions

Bioconductor version: 3.14

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>

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

Installation

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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Epigenetics, Genetics, HiddenMarkovModel, ImmunoOncology, NucleosomePositioning, Software
Version	1.12.0
In Bioconductor since	BioC 3.8 (R-3.5) (5.5 years)
License	file LICENSE
Depends	R (>= 3.6)
Imports	graphics, methods
System Requirements
URL

Suggests	NuPoP, Biostrings, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	nuCpos_1.12.0.tar.gz
Windows Binary	nuCpos_1.12.0.zip
macOS 10.13 (High Sierra)	nuCpos_1.12.0.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 3.14	Source Archive