cubfits: Codon Usage Bias Fits
Version 0.1-3

Estimating mutation and selection coefficients on synonymous codon bias usage based on models of ribosome overhead cost (ROC). Multinomial logistic regression and Markov Chain Monte Carlo are used to estimate and predict protein production rates with/without the presence of expressions and measurement errors. Work flows with examples for simulation, estimation and prediction processes are also provided with parallelization speedup. The whole framework is tested with yeast genome and gene expression data of Yassour, et al. (2009) .

Getting started

Package details

AuthorWei-Chen Chen [aut, cre], Russell Zaretzki [aut], William Howell [aut], Cedric Landerer [aut], Drew Schmidt [aut], Michael A. Gilchrist [aut], Preston Hewgley [ctb], Students REU13 [ctb]
Date of publication2017-04-30 21:43:54 UTC
MaintainerWei-Chen Chen <[email protected]>
LicenseMozilla Public License 2.0
Version0.1-3
URL https://github.com/snoweye/cubfits
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("cubfits")

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cubfits documentation built on May 29, 2017, 5:32 p.m.