Package: cubfits 0.1-4
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>.
Authors:
cubfits_0.1-4.tar.gz
cubfits_0.1-4.zip(r-4.5)cubfits_0.1-4.zip(r-4.4)cubfits_0.1-4.zip(r-4.3)
cubfits_0.1-4.tgz(r-4.4-x86_64)cubfits_0.1-4.tgz(r-4.4-arm64)cubfits_0.1-4.tgz(r-4.3-x86_64)cubfits_0.1-4.tgz(r-4.3-arm64)
cubfits_0.1-4.tar.gz(r-4.5-noble)cubfits_0.1-4.tar.gz(r-4.4-noble)
cubfits_0.1-4.tgz(r-4.4-emscripten)cubfits_0.1-4.tgz(r-4.3-emscripten)
cubfits.pdf |cubfits.html✨
cubfits/json (API)
| # Install 'cubfits' in R: |
| install.packages('cubfits', repos = c('https://snoweye.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/snoweye/cubfits/issues
- .CF.AC - Default Controlling Options
- .CF.CONF - Default Controlling Options
- .CF.CT - Default Controlling Options
- .CF.DP - Default Controlling Options
- .CF.GV - Default Controlling Options
- .CF.OP - Default Controlling Options
- .CF.PARAM - Default Controlling Options
- .CF.PT - Default Controlling Options
- .CO.CT - Default Controlling Options
- .cubfitsEnv - Default Controlling Options
- b.Init - Datasets for Demonstrations
- ex.test - Datasets for Demonstrations
- ex.train - Datasets for Demonstrations
- yassour - Yassour 2009 Yeast Experiment Dataset
- yassour.PM.appr - Posterior Results of Yassour 2009 Yeast Experiment Dataset
- yassour.PM.fits - Posterior Results of Yassour 2009 Yeast Experiment Dataset
- yassour.info - Posterior Results of Yassour 2009 Yeast Experiment Dataset
Last updated 3 years agofrom:7462d9f475. Checks:OK: 5 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 12 2024 |
| R-4.5-win-x86_64 | OK | Sep 12 2024 |
| R-4.5-linux-x86_64 | OK | Sep 12 2024 |
| R-4.4-win-x86_64 | OK | Sep 12 2024 |
| R-4.4-mac-x86_64 | NOTE | Sep 12 2024 |
| R-4.4-mac-aarch64 | NOTE | Sep 12 2024 |
| R-4.3-win-x86_64 | OK | Sep 12 2024 |
| R-4.3-mac-x86_64 | NOTE | Sep 12 2024 |
| R-4.3-mac-aarch64 | NOTE | Sep 12 2024 |
Exports:asl.optimcalc_cai_valuescalc_scu_valuescalc_scuo_valuescodon.low2upcodon.up2lowconvert.b.to.bVecconvert.bVec.to.bconvert.n.to.listconvert.reu13.df.to.listconvert.seq.data.to.stringconvert.y.to.listconvert.y.to.scuocp.workflowcubapprcubfitscubmultichaincubpredcubsinglechaindasldasladmixnormerrdna.low2updna.up2lowestimatePhifitMultinomgen.ngen.phi.Obsgen.reu13.dfgen.reu13.listgen.scuogen.yget.expathget.workflowinit.functionmixnormerr.optimnormalizeDataSetpaslpaslaplotaddmodelplotbinplotbin.NSEplotBMatrixPosteriorplotCUBplotCUB.NSEplotExpectedPhiTraceplotmodelplotprxyplotPTracesplotTracesprop.bin.rocprop.model.nseprop.model.rocqaslqaslaraslraslaread.phi.dfread.seqreadGenomerearrange.nrearrange.phi.Obsrearrange.reu13.dfrearrange.yscuo.randomsimu.mixnormerrsimu.orfsimu.phi.Obswrite.phi.dfwrite.seq
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Codon Bias Usage Fits | cubfits-package |
| The Asymmetric Laplace Distribution | asl.optim dasl dasla pasl pasla qasl qasla rasl rasla |
| Cedric Convergence Utilities | cubmultichain cubsinglechain isConverged |
| Cedric IO Utilities | normalizeDataSet readGenome |
| Cedric Plot Utilities | plotCUB plotExpectedPhiTrace plotPTraces plotTraces |
| Function for Codon Adaptation Index (CAI) | calc_cai_values |
| Default Controlling Options | .CF.AC .CF.CONF .CF.CT .CF.DP .CF.GV .CF.OP .CF.PARAM .CF.PT .CO.CT .cubfitsEnv |
| Convert Data Frame to Other Formats | codon.low2up codon.up2low convert.b.to.bVec convert.bVec.to.b convert.n.to.list convert.reu13.df.to.list convert.seq.data.to.string convert.y.to.list convert.y.to.scuo DataConverting dna.low2up dna.up2low |
| Codon Usage Bias Approximation for ORFs without Expression | cubappr |
| Codon Usage Bias Fits for Observed ORFs and Expression | cubfits |
| Codon Usage Bias Prediction for Observed ORFs | cubpred |
| Data Formats | AllDataFormats b bVec n n.list phi.df phi.Obs reu13.df reu13.list scuo seq.data seq.string y y.list |
| Datasets for Demonstrations | b.Init ex.test ex.train |
| Initialization of Phi (Generic) | estimatePhi |
| Fit Multinomial Model (Generic) | fitMultinom |
| Generating Data Structure | DataGenerating gen.n gen.phi.Obs gen.reu13.df gen.reu13.list gen.scuo gen.y |
| Initial Generic Functions of Codon Usage Bias Fits | init.function |
| Input and Output Utility | DataIO get.expath read.phi.df read.seq write.phi.df write.seq |
| Mixed Normal Optimization | dmixnormerr mixnormerr.optim |
| Plot Binning Results | plotbin prop.bin.roc |
| Plot Fitted Models | plotaddmodel plotmodel prop.model.roc |
| Predictive X-Y Plot | plotprxy |
| Posterior Results of Yassour 2009 Yeast Experiment Dataset | yassour.info yassour.PM.appr yassour.PM.fits |
| Functions for Printing Objects According to Classes | print.mixnormerr |
| Generate Randomized SCUO Index | scuo.random |
| Rearrange Data Structure by ORF Names | rearrange.n rearrange.phi.Obs rearrange.reu13.df rearrange.y |
| Function for Synonymous Codon Usage Order (SCUO) Index | calc_scuo_values |
| Function for Selection on Codon Usage (SCU) | calc_scu_values |
| Simulate ORFs and Expression Data | simu.mixnormerr simu.orf simu.phi.Obs |
| Yassour 2009 Yeast Experiment Dataset | yassour |
