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>

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

Details

biocViews Epigenetics, Genetics, HiddenMarkovModel, ImmunoOncology, NucleosomePositioning, Software
Version 1.10.0
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
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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_1.10.0.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
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 3.13 Source Archive