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

An R package for nucleosome positioning prediction

Bioconductor version: Development (3.19)

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 (from within R, enter citation("NuPoP")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

NuPoP HTML R Script
Reference Manual PDF


biocViews Classification, Genetics, HiddenMarkovModel, NucleosomePositioning, Software, Visualization
Version 2.11.0
In Bioconductor since BioC 2.7 (R-2.12) (13.5 years)
License GPL-2
Depends R (>= 4.0)
Imports graphics, utils
System Requirements
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Suggests knitr, rmarkdown
Linking To
Depends On Me
Imports Me
Suggests Me nuCpos
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package NuPoP_2.11.0.tar.gz
Windows Binary NuPoP_2.11.0.zip
macOS Binary (x86_64) NuPoP_2.11.0.tgz
macOS Binary (arm64) NuPoP_2.11.0.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/
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