Man pages for cubfits
Codon Usage Bias Fits
| 00_cubfits-package | Codon Bias Usage Fits |
| a1_cubfits | Codon Usage Bias Fits for Observed ORFs and Expression |
| a2_cubappr | Codon Usage Bias Approximation for ORFs without Expression |
| a3_cubpred | Codon Usage Bias Prediction for Observed ORFs |
| b0_plotprxy | Predictive X-Y Plot |
| b1_plotbin | Plot Binning Results |
| b2_plotmodel | Plot Fitted Models |
| c0_plot | Cedric Plot Utilities |
| c1_io | Cedric IO Utilities |
| c2_convergence | Cedric Convergence Utilities |
| c9_internal | All Cedric Internal Functions |
| s0_init.function | Initial Generic Functions of Codon Usage Bias Fits |
| s1_fitMultinom | Fit Multinomial Model (Generic) |
| s2_estimatePhi | Initialization of Phi (Generic) |
| t1_simulation | Simulate ORFs and Expression Data |
| t2_scuo | Function for Synonymous Codon Usage Order (SCUO) Index |
| t3_scuo.random | Generate Randomized SCUO Index |
| t4_cai | Function for Codon Adaptation Index (CAI) |
| t5_scu | Function for Selection on Codon Usage (SCU) |
| u0_io | Input and Output Utility |
| u1_gen | Generating Data Structure |
| u2_convert | Convert Data Frame to Other Formats |
| u3_rearrange | Rearrange Data Structure by ORF Names |
| u4_asl | The Asymmetric Laplace Distribution |
| u5_mixnorm | Mixed Normal Optimization |
| vv_print | Functions for Printing Objects According to Classes |
| xx_dataformat | Data Formats |
| yy_control | Default Controlling Options |
| yy_dataset | Datasets for Demonstrations |
| yy_yassour | Yassour 2009 Yeast Experiment Dataset |
| yy_yassour_PM | Posterior Results of Yassour 2009 Yeast Experiment Dataset |
| zz_internal | All Internal Functions |
