Package: nuCpos
Title: An R package for prediction of nucleosome positions
Authors@R: c(person("Hiroaki", "Kato", role=c("aut", "cre"), 
			email="hkato@med.shimane-u.ac.jp"), 
		person("Takeshi", "Urano", role=c("ctb")))
Version: 1.16.0
Description: 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
License: GPL-2
Depends: R (>= 4.2.0)
Imports: graphics, methods
Suggests: NuPoP, Biostrings, testthat
biocViews: Genetics, Epigenetics, NucleosomePositioning,
        HiddenMarkovModel, ImmunoOncology
Date: 2022-08-10
NeedsCompilation: yes
git_url: https://git.bioconductor.org/packages/nuCpos
git_branch: RELEASE_3_16
git_last_commit: ceba3ff
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
Packaged: 2022-11-01 22:14:03 UTC; biocbuild
Maintainer: Hiroaki Kato <hkato@med.shimane-u.ac.jp>
Built: R 4.2.1; x86_64-conda-linux-gnu; 2022-11-03 08:11:27 UTC; unix
