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| ddepn-package | Dynamic Deterministic Effects Propagation Networks: Infer signalling networks from high througput array data. |
| addstimuli | Add dummy stimulus nodes to the data matrix. |
| bestgam | Fit an optimal smoothing spline to a data vector y, indexed by time vector tp. |
| calcpr | Calculate a structure prior. Usually called internally. |
| center_ddepn | Perform centering of single replicate time courses. |
| cls | DDEPN function tests. |
| compare.graphs.tc | compare.graphs.tc |
| create_signetwork | inhibMCMC Analysis: find significant edges from independent MCMC chains |
| create_signetwork_cv | inhibMCMC Analysis: find significant edges from independent MCMC chains |
| ddepn | ddepn |
| draw_segments | inhibMCMC Analysis: find significant edges from independent MCMC chains |
| esub | Fit an optimal smoothing spline to a data vector y, indexed by time vector tp. |
| format_ddepn | Performs renaming of the colnames of dataset hcc1954 to make it suitable as input for the inference. |
| gelman_diag | Convergence check by Gelman's potential scale reduction. |
| get.arrowhead | plotdetailed get.labels get.arrowhead get.arrowtail |
| get.arrowtail | plotdetailed get.labels get.arrowhead get.arrowtail |
| get.labels | plotdetailed get.labels get.arrowhead get.arrowtail |
| get.phi.final | Construct final network from GA or mcmc result. |
| get.phi.final.mcmc | Construct final network from GA or mcmc result. |
| get_theta_consensus | Plot the data and inferred model parameters. |
| hcc1954 | hcc1954 |
| hcc1954fcf | hcc1954 |
| hcc1954fcfmedian | hcc1954 |
| hcc1954raw | hcc1954 |
| kegggraph.to.detailed.adjacency | kegggraph.to.detailed.adjacency |
| kegggraphs | kegggraphs |
| makedata | Generate artificial dataset given a network and list of stimuli. |
| make_edge_df | Boxplots of edge confidences obtained in inhibMCMC. |
| mcmc_ddepn | mcmc_ddepn - Perform MCMC sampling for DDEPN. |
| netga | netga - Perform network search using a genetic algorithm. |
| perform_edge_test | inhibMCMC Analysis: find significant edges from independent MCMC chains |
| perform_network_tests | inhibMCMC Analysis: find significant edges from independent MCMC chains |
| plotdetailed | plotdetailed get.labels get.arrowhead get.arrowtail |
| plotrepresult | Plot result of reconstruction. |
| plot_edgeconfidences | Boxplots of edge confidences obtained in inhibMCMC. |
| plot_mcmctraces | Trace plot for inhibMCMC posterior traces. |
| plot_profiles | Plot the data and inferred model parameters. |
| prior | Calculate a structure prior. Usually called internally. |
| resume_ddepn | ddepn |
| runmcmc | mcmc_ddepn - Perform MCMC sampling for DDEPN. |
| run_checks | DDEPN function tests. |
| signalnetwork | Sample a random signalling network. |
| simulatedata | simulatedata |
| wrapddepn | DDEPN function tests. |