DOI: 10.18129/B9.bioc.nuCpos  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see nuCpos.

An R package for prediction of nucleosome positions

Bioconductor version: 3.16

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. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provide chemical-map-based prediction, users are strongly encouraged to use it for dHMM-based prediction.

Author: Hiroaki Kato, Takeshi Urano

Maintainer: Hiroaki Kato <hkato at>

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


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biocViews Epigenetics, Genetics, HiddenMarkovModel, ImmunoOncology, NucleosomePositioning, Software
Version 1.16.3
In Bioconductor since BioC 3.8 (R-3.5) (4.5 years)
License GPL-2
Depends R (>= 4.2.0)
Imports graphics, methods
Suggests NuPoP, Biostrings, testthat
Depends On Me
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