Man pages for CoRegFlux
CoRegFlux
| adjust_constraints_to_observed_rates | Adjust the constraint of the model to observed rates |
| aliases_SC | aliases_SC data |
| build_exchange_met | Build the exchange metabolite data.frame |
| continuous_gpr | Continuous evaluation of the gpr rules |
| convert_metabolites_to_model_names | Convert metabolites name to the model equivalent |
| coregflux_static | Update the model using the provided gene regulatory network... |
| euler_step_biomass | Euler step biomass |
| euler_step_metabolites | Compute the metabolite concentrations at the next time point |
| FBA_step | Flux balance analysis solution for the model |
| get_biomass_flux_position | Get biomass flux position |
| get_fba_fluxes_from_observations | Get fluxes balance from an observed growth rate |
| get_fva_intervals_from_observations | Get intervals of flux variability (FVA) from an observed... |
| get_linear_model | Train a linear model |
| get_metabolites_exchange_fluxes | Get metabolites exchange fluxes |
| gpr_expression | Transform a logic gpr rule string to a list and then evaluate... |
| iMM904 | iMM904 |
| ODCurveToFluxCurves | ODCurveToFluxCurves |
| ODCurveToMetabolicGeneCurves | ODCurveToMetabolicGeneCurves |
| ODcurveToMetCurve | ODcurveToMetCurve data |
| ODtoflux | ODtoflux data |
| ODToFluxBounds | ODToFluxBounds |
| perturbation_function | Perturbation function |
| PredictedGeneState | PredictedGeneState data |
| predict_linear_model_influence | Predict the gene expression level based on condition-specific... |
| SC_EXP_DATA | SC_EXP_DATA data |
| SC_experiment_influence | SC_experiment_influence data |
| SC_GRN_1 | SC_GRN_1 data |
| SC_Test_data | SC_Test_data data |
| Simulation | Simulation using Dynamic Flux balance analysis over time as... |
| Simulation_Step | Single simulation step |
| train_continuous_model | Train a linear model and predict the gene expression from an... |
| update_fluxes_constraints_geneKOOV | Update the fluxes constraints to simulate gene KO or... |
| update_fluxes_constraints_GRegulation | Update fluxes constraints |
| update_fluxes_constraints_influence | Update the fluxes constraints to simulate TF KO or... |
| update_fluxes_state | Update the fluxes bounds given the metabolites concentrations |
| update_system_state | Update the fluxes, metabolites concentration and biomass in... |
| update_uptake_fluxes_constraints_metabolites | Update the fluxes constraints given the metabolite... |
| visFluxCurves | Visualize Fluxes Curves |
| visMetabolicGeneCurves | Visualize Metabolic Gene Curves |
