nuCpos
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see nuCpos.
An R package for prediction of nucleosome positions
Bioconductor version: 3.9
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("nuCpos")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Epigenetics, Genetics, HiddenMarkovModel, ImmunoOncology, NucleosomePositioning, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.5.1) |
| 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_1.2.0.tar.gz |
| Windows Binary | nuCpos_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | nuCpos_1.2.0.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 3.9 | Source Archive |