nuCpos

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see nuCpos.

An R package for prediction of nucleosome positions


Bioconductor version: 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>

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

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

Details

biocViews Epigenetics, Genetics, HiddenMarkovModel, ImmunoOncology, NucleosomePositioning, Software
Version 1.16.3
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-2
Depends R (>= 4.2.0)
Imports graphics, methods
System Requirements
URL
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Suggests NuPoP, Biostrings, testthat
Linking To
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Depends On Me
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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