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cubfits (version 0.1-2)

Codon Usage Bias Fits

Description

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).

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Install

install.packages('cubfits')

Monthly Downloads

708

Version

0.1-2

License

Mozilla Public License 2.0

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Last Published

January 24th, 2016

Functions in cubfits (0.1-2)

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