nuCpos

DOI: 10.18129/B9.bioc.nuCpos    

An R package for prediction of nucleosome positions

Bioconductor version: Release (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("nuCpos", version = "3.8")

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
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Details

biocViews Epigenetics, Genetics, HiddenMarkovModel, NucleosomePositioning, Software
Version 1.0.0
License GPL-2
Depends R (>= 3.5.1)
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_1.0.0.tar.gz
Windows Binary nuCpos_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) nuCpos_1.0.0.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 http://bioconductor.org/packages/nuCpos/
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