API for saezlab/PHONEMeS-ILP
Building logic-based models from discovery high-content phosphoproteomics data
| Global functions | |
|---|---|
| BMsim | Man page Source code |
| GMMbyCond | Man page |
| GMMbyCond-class | Man page |
| GMMres | Man page |
| GMMres-class | Man page |
| ModelList | Man page |
| ModelList-class | Man page |
| OptParam | Man page |
| OptParam-class | Man page |
| PHONEMeS | Man page |
| PHONEMeS-package | Man page |
| PKN_list | Source code |
| PKNlist | Man page Man page Source code |
| PKNlist-class | Man page |
| all_constraints | Source code |
| assignAttributes | Man page Source code |
| assignAttributes_tp | Source code |
| assign_tp_attributes | Source code |
| buildDataMatrix | Source code |
| buildDataObject | Source code |
| buildInputs | Man page Source code |
| buildNetwork | Source code |
| buildNw | Man page Source code |
| buildPKN | Man page Source code |
| build_Nw | Source code |
| build_Nw_Inv | Source code |
| build_PKN | Source code |
| build_PKN_Inv | Source code |
| checkInputs | Source code Source code |
| combine_networks | Source code |
| createModel | Man page Source code |
| createSIF | Source code |
| create_binaries | Source code |
| create_binary_variables_for_x_vector | Source code |
| create_binary_variables_for_y_vector | Source code |
| create_binary_variables_for_z_vector | Source code |
| create_orin_orout_variables | Source code |
| dataBycond | Man page Source code |
| dataTable | Man page Source code |
| integratorWeights | Man page Source code |
| intermediateWeights | Man page Source code |
| mInw | Man page Source code |
| makeContrastsAlt | Source code Source code |
| nodeAttr | Man page Source code |
| nodesData | Man page Source code |
| normalise | Source code |
| oRes | Man page Source code |
| pathsD | Man page Source code |
| plotoRes | Man page Source code |
| poolContrasts | Source code |
| readOutSIF | Source code |
| readOutSIFAll | Source code |
| removeRedundantEdges | Source code |
| removeRedundantNodes | Source code |
| run1model | Man page Source code |
| runLimma | Man page Source code Source code |
| runPHONEMeS | Man page Source code |
| runPHONEMeS_Downsampling | Man page Source code |
| runPHONEMeS_UD | Man page Source code |
| runPHONEMeS_mult | Man page Source code |
| simulateT1 | Man page Source code |
| sinkWeights | Man page Source code |
| solve_with_cbc | Source code |
| solve_with_cplex | Source code |
| solve_with_cplex_downsampling | Source code |
| solve_with_cplex_tp | Source code |
| ttopFormatter | Source code Source code |
| writeFile | Source code |
| write_boundaries | Source code |
| write_constraints_1 | Source code |
| write_constraints_2 | Source code |
| write_constraints_2_ud | Source code |
| write_constraints_3 | Source code |
| write_constraints_4 | Source code |
| write_constraints_5 | Source code |
| write_constraints_5_ud | Source code |
| write_equality_constraints | Source code |
| write_in_out_constraints | Source code |
| write_lp_file | Source code |
| write_lp_file_1 | Source code |
| write_lp_file_2 | Source code |
| write_lp_file_downsampling | Source code |
| write_lp_file_inv_1 | Source code |
| write_lp_file_inv_2 | Source code |
| write_objective_function | Source code |
| write_self_activating_constraints | Source code |
| write_time_point_constraints | Source code |
