Package: nuCpos
Title: An R package for prediction of nucleosome positions
Version: 1.12.0
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. 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@med.shimane-u.ac.jp>
License: file LICENSE
Depends: R (>= 3.6)
Imports: graphics, methods
Suggests: NuPoP, Biostrings, testthat
biocViews: Genetics, Epigenetics, NucleosomePositioning,
        HiddenMarkovModel, ImmunoOncology
Date: 2019-11-08
NeedsCompilation: yes
git_url: https://git.bioconductor.org/packages/nuCpos
git_branch: RELEASE_3_14
git_last_commit: ff31780
git_last_commit_date: 2021-10-26
Date/Publication: 2021-10-26
Packaged: 2021-10-26 22:04:35 UTC; biocbuild
Built: R 4.1.1; x86_64-apple-darwin13.4.0; 2021-11-01 22:40:46 UTC; unix
