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>

Citation (from within R, enter citation("nuCpos")):


To install this package, start R (version "3.5") and enter:

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

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:



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biocViews Epigenetics, Genetics, HiddenMarkovModel, NucleosomePositioning, Software
Version 1.0.0
License GPL-2
Depends R (>= 3.5.1)
Imports graphics, methods
Suggests NuPoP, Biostrings, testthat
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package nuCpos_1.0.0.tar.gz
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Mac OS X 10.11 (El Capitan) nuCpos_1.0.0.tgz
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