cubfits: Codon Usage Bias Fits

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) <doi:10.1073/pnas.0812841106>.

Version:	0.1-4
Depends:	R (≥ 4.0.0), methods, coda, foreach, parallel, stats, graphics, utils
Suggests:	seqinr, VGAM, EMCluster
Enhances:	pbdMPI (≥ 0.3-1)
Published:	2021-11-07
DOI:	10.32614/CRAN.package.cubfits
Author:	Wei-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]
Maintainer:	Wei-Chen Chen <wccsnow at gmail.com>
BugReports:	https://github.com/snoweye/cubfits/issues
License:	Mozilla Public License 2.0
URL:	https://github.com/snoweye/cubfits
NeedsCompilation:	yes
Citation:	cubfits citation info
Materials:	README ChangeLog INSTALL
In views:	Omics
CRAN checks:	cubfits results

Documentation:

Reference manual:	cubfits.pdf
Vignettes:	cubfits-guide

Downloads:

Package source:	cubfits_0.1-4.tar.gz
Windows binaries:	r-devel: cubfits_0.1-4.zip, r-release: cubfits_0.1-4.zip, r-oldrel: cubfits_0.1-4.zip
macOS binaries:	r-release (arm64): cubfits_0.1-4.tgz, r-oldrel (arm64): cubfits_0.1-4.tgz, r-release (x86_64): cubfits_0.1-4.tgz, r-oldrel (x86_64): cubfits_0.1-4.tgz
Old sources:	cubfits archive

Linking:

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