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nuCpos

This is the development version of nuCpos; for the stable release version, see nuCpos.

An R package for prediction of nucleosome positions


Bioconductor version: Development (3.20)

nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. nuCpos calculates local and whole nucleosomal histone binding affinity (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 provides chemical-map-based prediction, the function for dHMM-based prediction was removed from this package. nuCpos continues to provide functions for HBA calculation.

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 "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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, NucleosomePositioning, Software
Version 1.23.0
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
See More
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_1.23.0.tar.gz
Windows Binary nuCpos_1.23.0.zip (64-bit only)
macOS Binary (x86_64) nuCpos_1.23.0.tgz
macOS Binary (arm64) nuCpos_1.23.0.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