Man pages for cubfits
Codon Usage Bias Fits

00_cubfits-packageCodon Bias Usage Fits
a1_cubfitsCodon Usage Bias Fits for Observed ORFs and Expression
a2_cubapprCodon Usage Bias Approximation for ORFs without Expression
a3_cubpredCodon Usage Bias Prediction for Observed ORFs
b0_plotprxyPredictive X-Y Plot
b1_plotbinPlot Binning Results
b2_plotmodelPlot Fitted Models
c0_plotCedric Plot Utilities
c1_ioCedric IO Utilities
c2_convergenceCedric Convergence Utilities
c9_internalAll Cedric Internal Functions
s0_init.functionInitial Generic Functions of Codon Usage Bias Fits
s1_fitMultinomFit Multinomial Model (Generic)
s2_estimatePhiInitialization of Phi (Generic)
t1_simulationSimulate ORFs and Expression Data
t2_scuoFunction for Synonymous Codon Usage Order (SCUO) Index
t3_scuo.randomGenerate Randomized SCUO Index
t4_caiFunction for Codon Adaptation Index (CAI)
t5_scuFunction for Selection on Codon Usage (SCU)
u0_ioInput and Output Utility
u1_genGenerating Data Structure
u2_convertConvert Data Frame to Other Formats
u3_rearrangeRearrange Data Structure by ORF Names
u4_aslThe Asymmetric Laplace Distribution
u5_mixnormMixed Normal Optimization
vv_printFunctions for Printing Objects According to Classes
xx_dataformatData Formats
yy_controlDefault Controlling Options
yy_datasetDatasets for Demonstrations
yy_yassourYassour 2009 Yeast Experiment Dataset
yy_yassour_PMPosterior Results of Yassour 2009 Yeast Experiment Dataset
zz_internalAll Internal Functions
cubfits documentation built on May 2, 2019, 4:08 a.m.