.cubfitsEnv             Default Controlling Options
b                       Data Formats
b.Init                  Datasets for Demonstrations
calc_cai_values         Function for Codon Adaptation Index (CAI)
calc_scu_values         Function for Selection on Codon Usage (SCU)
calc_scuo_values        Function for Synonymous Codon Usage Order
                        (SCUO) Index
convert.reu13.df.to.list
                        Convert Data Frame to Other Formats
cubappr                 Codon Usage Bias Approximation for ORFs without
                        Expression
cubfits                 Codon Usage Bias Fits for Observed ORFs and
                        Expression
cubfits-package         Codon Bias Usage Fits
cubmultichain           Cedric Convergence Utilities
cubpred                 Codon Usage Bias Prediction for Observed ORFs
dasl                    The Asymmetric Laplace Distribution
estimatePhi             Initialization of Phi (Generic)
fitMultinom             Fit Multinomial Model (Generic)
gen.reu13.df            Generating Data Structure
get.expath              Input and Output Utility
init.function           Initial Generic Functions of Codon Usage Bias
                        Fits
mixnormerr.optim        Mixed Normal Optimization
plotCUB                 Cedric Plot Utilities
plotprxy                Predictive X-Y Plot
print.mixnormerr        Functions for Printing Objects According to
                        Classes
prop.bin.roc            Plot Binning Results
prop.model.roc          Plot Fitted Models
readGenome              Cedric IO Utilities
rearrange.reu13.df      Rearrange Data Structure by ORF Names
scuo.random             Generate Randomized SCUO Index
simu.orf                Simulate ORFs and Expression Data
yassour                 Yassour 2009 Yeast Experiment Dataset
yassour.PM.fits         Posterior Results of Yassour 2009 Yeast
                        Experiment Dataset
