# cubfits v0.1-2

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## 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 (2009).

## Functions in cubfits

Name | Description | |

Cedric Plot Utilities | Cedric Plot Utilities | |

Datasets | Datasets for Demonstrations | |

Estimate Phi | Initialization of Phi (Generic) | |

Plotprxy | Predictive X-Y Plot | |

CUB Model Prediction | Codon Usage Bias Prediction for Observed ORFs | |

CUB Model Fits | Codon Usage Bias Fits for Observed ORFs and Expression | |

Generating Utility | Generating Data Structure | |

Controls | Default Controlling Options | |

Selection on Codon Usage | Function for Selection on Codon Usage (SCU) | |

Asymmetric Laplace Distribution | The Asymmetric Laplace Distribution | |

cubfits-package | Codon Bias Usage Fits | |

Simulation Tool | Simulate ORFs and Expression Data | |

Cedric Internal Functions | All Cedric Internal Functions | |

SCUO Index | Function for Synonymous Codon Usage Order (SCUO) Index | |

Initial Generic Functions | Initial Generic Functions of Codon Usage Bias Fits | |

Codon Adaptation Index | Function for Codon Adaptation Index (CAI) | |

Posterior Results of Yassour2009 | Posterior Results of Yassour 2009 Yeast Experiment Dataset | |

Plotmodel | Plot Fitted Models | |

Input and Output Utility | Input and Output Utility | |

Data Formats | Data Formats | |

Functions for Printing Objects According to Classes | ||

Fit Multinomial | Fit Multinomial Model (Generic) | |

Coverting Utility | Convert Data Frame to Other Formats | |

Yassour2009 | Yassour 2009 Yeast Experiment Dataset | |

Randomize SCUO Index | Generate Randomized SCUO Index | |

Mixed Normal Optimization | Mixed Normal Optimization | |

Rearrangment Utility | Rearrange Data Structure by ORF Names | |

Cedric IO Utilities | Cedric IO Utilities | |

Cedric Convergence Utilities | Cedric Convergence Utilities | |

Plotbin | Plot Binning Results | |

Internal Functions | All Internal Functions | |

CUB Model Approximation | Codon Usage Bias Approximation for ORFs without Expression | |

No Results! |

## Last month downloads

## Details

Date | 2016-01-24 |

LazyLoad | yes |

LazyData | yes |

License | Mozilla Public License 2.0 |

URL | https://github.com/snoweye/cubfits |

NeedsCompilation | yes |

Packaged | 2016-01-24 20:10:27 UTC; snoweye |

Repository | CRAN |

Date/Publication | 2016-01-24 21:39:07 |

depends | base (>= 3.0.0) , coda , foreach , graphics , methods , parallel , R (>= 3.0.0) , stats , utils |

suggests | EMCluster , seqinr , VGAM |

enhances | pbdMPI (>= 0.3-1) |

Contributors | Drew Schmidt, Wei-Chen Chen, Russell Zaretzki, William Howell, Students REU13, Cedric Landerer, Michael A. Gilchrist, Preston Hewgley |

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