nuCpos: An R package for prediction of nucleosome positions

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.

Package details

AuthorHiroaki Kato, Takeshi Urano
Bioconductor views Epigenetics Genetics HiddenMarkovModel ImmunoOncology NucleosomePositioning
MaintainerHiroaki Kato <hkato@med.shimane-u.ac.jp>
Licensefile LICENSE
Version1.6.0
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("nuCpos")

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nuCpos documentation built on April 29, 2020, 6:21 a.m.