cubfits v0.1-2

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by Wei-Chen Chen

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
Print 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
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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

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