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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 |
| 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 |
| Reference manual: | cubfits.pdf |
| Vignettes: |
cubfits-guide |
| 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 |
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