Man pages for DikshantPradhan/FluxCouplingTools
| add_exch_rxns_to_model | add exchange reactions for metabolites in indicated reaction... |
| check_sets_for_containing | check to see if set list contains elements of interest |
| clean_rxn_names_in_set | process names of coupled reactions to replace the names of... |
| combine_tables | combine two tables |
| compare_sets | return T/F based on whether or not two set-lists are... |
| convert_sybil_to_gurobi | description |
| coupling_matrix_from_coupling_vector_list | Convert the output of GRB_generate_set_lists_cluster to a... |
| fill_coupling_matrix_from_sets | given a boolean coupling matrix, ensure that all reactions in... |
| find_composing_sets | find the sets contained by 'rxns' |
| flux_coupling_raptor | determine flux coupling between reactions in a Gurobi model |
| generate_falcon_model | Generate FALCON model from base metabolic Sybil model |
| generate_gpr | generate GPR dataframe |
| gene_set_from_rxn_set | extrapolate a gene set from a reaction set based on GPR |
| get_containing_set_idx | get the position of the set containing all members of a group... |
| get_ecoli_model | description |
| get_genes_from_react_id | identify all genes associated with a reaction |
| get_list_of_sets_from_mtx | generate sets from coupling mtx |
| get_mutans_model | generate Streptococcus mutans model |
| get_PAO_model | generate Pseudomonas Aeruginosa model |
| get_set_idx | get position of the set containing an element in a list of... |
| get_yeast_maranas_model | generate Saccharomyces cerevisiae model |
| GRB_ecoli_falcon_model | description |
| GRB_ecoli_model | description |
| GRB_flux_coupling_raptor_wrapper | wrapper function for flux coupling |
| GRB_generate_falcon_model | Generate Gurobi falcon model. First generates model in sybil... |
| GRB_generate_set_lists_cluster | Function for PACT method |
| GRB_get_rxn_idx | get the position of a reaction along its axis on the S matrix |
| GRB_maximize | flux-balance optimization function for Gurobi |
| GRB_mutans_falcon_model | Gurobi S. mutans falcon model |
| GRB_mutans_model | Gurobi S. mutans model |
| GRB_pao_falcon_model | Gurobi P. aeruginosa falcon model |
| GRB_pao_model | Gurobi P. aeruginosa model |
| GRB_yeast_falcon_model | Gurobi S. cerevisiae falcon model |
| GRB_yeast_model | Gurobi S. cerevisiae model |
| identify_intermediate_uncoupled | identify which G sets and R sets within the same G* or R* set... |
| isolate_gene_matrix | reduce coupling matrix to only contain the reactions for... |
| isolate_rxn_matrix | reduce coupling matrix to only the metabolic reactions |
| optimize_rxn | minimize or maximize flux through a reaction in a given... |
| read_coupling_csv | Read in coupling file |
| set_model_bounds | change the bounds on a Gurobi model |
| solve_model | Solve Gurobi model |
