NuPoP
An R package for nucleosome positioning prediction
Bioconductor version: Release (3.17)
NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.
Author: Ji-Ping Wang <jzwang at northwestern.edu>; Liqun Xi <liqunxi02 at gmail.com>; Oscar Zarate <zarate at u.northwestern.edu>
Maintainer: Ji-Ping Wang<jzwang at northwestern.edu>
citation("NuPoP")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("NuPoP")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("NuPoP")| NuPoP | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Genetics, HiddenMarkovModel, NucleosomePositioning, Software, Visualization |
| Version | 2.8.1 |
| In Bioconductor since | BioC 2.7 (R-2.12) (13 years) |
| License | GPL-2 |
| Depends | R (>= 4.0) |
| Imports | graphics, utils |
| Linking To | |
| Suggests | knitr, rmarkdown |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | nuCpos |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | NuPoP_2.8.1.tar.gz |
| Windows Binary | NuPoP_2.8.1.zip |
| macOS Binary (x86_64) | NuPoP_2.8.1.tgz |
| macOS Binary (arm64) | NuPoP_2.8.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/NuPoP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NuPoP |
| Bioc Package Browser | https://code.bioconductor.org/browse/NuPoP/ |
| Package Short Url | https://bioconductor.org/packages/NuPoP/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |