Man pages for VladoBaca/BNRewiringRobustness
Discrete Bifurcation Analysis and Rewiring Robustness of Asynchronous Boolean Networks
| all_binary_vectors | Create the list of all the possible binary vectors of given... |
| bifurcation_plot | Draws the bifurcation plot for the given data |
| binary_vector_to_number | Get the number represented by binary vector (from most to... |
| binary_vector_to_one_based_index | Get the 1-based index of a binary vector representing a row... |
| build_transition_table | Build the transition table in the form of an matrix: row =... |
| compute_activity_ratios_matrix | Computes matrix of activity ratios (output genes x... |
| compute_attractor_distribution_matrix | Compute the async attractor distributions of all states in a... |
| compute_attractor_distribution_similarity | Computes the attractor distribution similarity using LP |
| compute_attractor_landscape_similarity | Computes attractor landscape similarity for two given... |
| compute_attractor_membership_vector | Get the vector of states membership in attractors. |
| compute_attractors_output_states_ratios_matrix | Computes matrix of output states ratios (output states x... |
| compute_attractors_similarity_matrix | Computes matrix of similarities for two given sets of... |
| compute_attractors_similarity_matrix_activity | Computes matrix of activity similarities for two given sets... |
| compute_attractors_similarity_matrix_overlap | Computes matrix of overlap similarities for two given sets of... |
| compute_constraints_coefficients_matrix | Computes the matrix of constrain coefficients for LP... |
| compute_conversion_vector | Compute the conversion vector for input genes of a given... |
| compute_db_single | The QDBF copmutation for one given parametrisation |
| compute_discrete_bifurcation | Computes the quantitative discrete bifurcation function of... |
| compute_discrete_bifurcation_inner | The inner computation of QDBF. |
| compute_intermediate_genes | Computes the set of transitive regulators of motif genes... |
| compute_rewiring_distance | Computes rewiring distance for two given parametrisations |
| compute_rewiring_robustness | Computes the phenotype rewiring robustness over the data... |
| compute_transition_table_cell | Compute value of one cell of transition table, given input... |
| compute_transition_table_row | Compute one row of transition table. |
| create_extension | Transform the given motif BN and possibly larger PBN to an... |
| create_intermediate_motif_parametrisation | Compute the parametrisation representing teh original motig... |
| create_intermediate_rg | Computes the motif extension from the given RG over given... |
| create_pbn_from_rg | Creates a PBN from given RG. |
| decode_attractor | Decode attractor from Boolnet into a vector of (binary)... |
| enumerate_gene_function_vectors | Enumerates all valid function vectors for given gene |
| extract_instance | Extract a BN instance from a PBN for a given index. |
| generate_BN | Generates a BooleanNetwork instance from the given data |
| generate_interaction | Generates a single interaction for genereated BN |
| generate_parametrisation_instance | Create a BN from a given parametrisation |
| get_attractor_landscape | Get the attractor landscape of a given parametrisation in the... |
| get_attractors_data_async | Get the list of attractors and the attractor probability... |
| get_attractors_data_sync | Get the list of attractors and the attractor probability... |
| get_function_vector | Get the function vector of given gene for the baseline... |
| get_parametrisation_by_index | Get a parametrisation from PBN by its numeric 1-based index. |
| get_parametrisation_by_index_combination_vector | Get a parametrisation from PBN by vector of indexes of update... |
| get_rg_genes | Get all the genes of the given RG. |
| is_function_vector_valid | Validates that given function vector satisfies the... |
| is_simple_string | Is the given input a normal string? |
| is_subset | Subset test |
| load_BN | Load the BoolNet Boolean network from the given .bn file. |
| load_PBN | Load the parametrised Boolean network from the RG in given... |
| load_RG | Load the Regulatory graph from the given file. |
| parallel_apply | Apply a function to all members of a collection parallelly. |
| prepare_parallel | Prepares the parallel execution. Creates a cluster for a... |
| pre_to_post_vector | Create the pre-to-post vector for decoding attractor states... |
| process_inputs | Process the inputs given to compute_discrete_bifurcation |
| validate_edges | Validate the proper relationship between the edges of motif... |
| validate_genes | Validate the proper relationship between the genes of output,... |
| validate_unique_edges | Validate that there are no repeating edges in the RG |
