Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | Z _ __init__() (corneto.data.Data method) (corneto.data.Sample method) (corneto.graph.BaseGraph method) (corneto.graph.Graph method) (corneto.methods.BidirectionalPHONEMeS method) (corneto.methods.CarnivalFlow method) (corneto.methods.CarnivalILP method) (corneto.methods.MultiSampleFBA method) (corneto.methods.MultiSampleIMAT method) (corneto.methods.PHONEMeS method) (corneto.methods.PrizeCollectingSteinerTree method) (corneto.methods.signaling.CellNOptDAG method) (corneto.methods.SteinerTreeFlow method) A Acyclic() (corneto.backend.Backend method) Acyclic0() (corneto.backend.Backend method) AcyclicFlow() (corneto.backend.Backend method) add() (corneto.data.Sample method) add_cellnopt_conditions() (in module corneto.methods.signaling) add_cellnopt_results() (in module corneto.methods.signaling) add_edge() (corneto.graph.BaseGraph method) add_edges() (corneto.graph.BaseGraph method) add_sample() (corneto.data.Data method) add_vertex() (corneto.graph.BaseGraph method) add_vertices() (corneto.graph.BaseGraph method) available_backends() (in module corneto.backend) available_solvers() (corneto.backend.Backend method) (corneto.backend.CvxpyBackend method) (corneto.backend.PicosBackend method) B Backend (class in corneto.backend) backend (corneto.methods.MultiSampleFBA attribute) BaseGraph (class in corneto.graph) beta_reg (corneto.methods.MultiSampleFBA attribute) bfs() (corneto.graph.BaseGraph method) BidirectionalPHONEMeS (class in corneto.methods) BINARY (corneto.backend.VarType attribute) build() (corneto.backend.Backend method) (corneto.backend.CvxpyBackend method) (corneto.backend.PicosBackend method) (corneto.methods.BidirectionalPHONEMeS method) (corneto.methods.MultiSampleFBA method) (corneto.methods.MultiSampleIMAT method) (corneto.methods.PHONEMeS method) (corneto.methods.PrizeCollectingSteinerTree method) (corneto.methods.signaling.CellNOptDAG method) (corneto.methods.SteinerTreeFlow method) build_cellnopt_from_annnet() (in module corneto.methods.signaling) build_dagnn() (in module corneto.ml) build_many() (corneto.methods.BidirectionalPHONEMeS method) (corneto.methods.MultiSampleFBA method) (corneto.methods.MultiSampleIMAT method) (corneto.methods.PHONEMeS method) (corneto.methods.PrizeCollectingSteinerTree method) (corneto.methods.signaling.CellNOptDAG method) (corneto.methods.SteinerTreeFlow method) C CarnivalFlow (class in corneto.methods) CarnivalILP (class in corneto.methods) CellNOptDAG (class in corneto.methods.signaling) cobra_model_to_graph() (in module corneto.io) compute_phonemes_scores() (in module corneto.methods) Constant() (corneto.backend.Backend method) (corneto.backend.CvxpyBackend method) (corneto.backend.PicosBackend method) CONTINUOUS (corneto.backend.VarType attribute) copy() (corneto.data.Data method) (corneto.graph.BaseGraph method) (corneto.graph.Graph method) corneto.backend module corneto.data module corneto.data.util module corneto.graph module corneto.io module corneto.methods module create_flow_based_problem() (corneto.methods.CarnivalFlow method) (corneto.methods.MultiSampleFBA method) (corneto.methods.MultiSampleIMAT method) (corneto.methods.PHONEMeS method) (corneto.methods.PrizeCollectingSteinerTree method) (corneto.methods.signaling.CellNOptDAG method) create_multisample_shortest_path() (in module corneto.methods) create_problem() (corneto.methods.BidirectionalPHONEMeS method) (corneto.methods.CarnivalILP method) (corneto.methods.PHONEMeS method) CvxpyBackend (class in corneto.backend) D Data (class in corneto.data) description() (corneto.methods.BidirectionalPHONEMeS static method) (corneto.methods.CarnivalFlow static method) (corneto.methods.PHONEMeS static method) (corneto.methods.signaling.CellNOptDAG static method) DIRECTED (corneto.graph.EdgeType attribute) disable_structured_sparsity (corneto.methods.MultiSampleFBA attribute) duplication_divergence_network() (in module corneto.graph) E E (corneto.graph.BaseGraph property) edge_subgraph() (corneto.graph.BaseGraph method) edges() (corneto.graph.BaseGraph method) EdgeType (class in corneto.graph) empty() (corneto.data.Data class method) extract_subgraph() (corneto.graph.BaseGraph method) (corneto.graph.Graph method) F features (corneto.data.Sample property) filter_graph() (corneto.graph.Graph method) Flow() (corneto.backend.Backend method) flux_indicator_name (corneto.methods.MultiSampleFBA attribute) from_cdict() (corneto.data.Data class method) from_cobra_model() (corneto.graph.Graph static method) from_dict() (corneto.data.Data class method) (corneto.data.Sample class method) (corneto.graph.Graph class method) from_json() (corneto.data.Data class method) (corneto.graph.Graph class method) from_miom_model() (corneto.graph.Graph static method) from_networkx() (corneto.graph.Graph static method) from_sif() (corneto.graph.Graph static method) from_sif_tuples() (corneto.graph.Graph static method) from_tuples() (corneto.graph.Graph static method) from_vertex_incidence() (corneto.graph.Graph static method) G generate_duplication_divergence_network() (in module corneto.data.util) generate_preferential_attachment_network() (in module corneto.data.util) generate_random_duplication_divergence_signalling_network() (in module corneto.data.util) generate_random_signalling_network() (in module corneto.data.util) get_attr_edge() (corneto.graph.BaseGraph method) get_attr_edges() (corneto.graph.BaseGraph method) get_attr_from_edges() (corneto.graph.BaseGraph method) get_attr_vertex() (corneto.graph.BaseGraph method) get_attr_vertices() (corneto.graph.BaseGraph method) get_common_incident_edges() (corneto.graph.BaseGraph method) get_edge() (corneto.graph.BaseGraph method) (corneto.graph.Graph method) get_edges() (corneto.graph.BaseGraph method) get_edges_by_attr() (corneto.graph.BaseGraph method) get_flow_bounds() (corneto.methods.BidirectionalPHONEMeS method) (corneto.methods.MultiSampleFBA method) (corneto.methods.PHONEMeS method) (corneto.methods.PrizeCollectingSteinerTree method) (corneto.methods.signaling.CellNOptDAG method) get_graph_attributes() (corneto.graph.BaseGraph method) (corneto.graph.Graph method) get_incident_edges() (corneto.graph.BaseGraph method) get_symbols() (corneto.backend.Backend static method) get_vertex() (corneto.graph.BaseGraph method) get_vertex_incidence_matrix_as_lists() (corneto.graph.BaseGraph method) Graph (class in corneto.graph) H hash() (corneto.graph.BaseGraph method) hstack() (corneto.backend.Backend method) I import_cobra_model() (in module corneto.io) import_miom_model() (in module corneto.io) in_edges() (corneto.graph.BaseGraph method) index_selector() (in module corneto.ml) Indicator() (corneto.backend.Backend method) INTEGER (corneto.backend.VarType attribute) is_available() (corneto.backend.Backend method) is_hypergraph() (corneto.graph.BaseGraph method) K kfold_nonzero_splits() (in module corneto.ml) L lambda_reg (corneto.methods.MultiSampleFBA attribute) linear_and() (corneto.backend.Backend method) linear_or() (corneto.backend.Backend method) linear_xor() (corneto.backend.Backend method) load() (corneto.data.Data class method) (corneto.graph.BaseGraph static method) load_graph_from_sif() (in module corneto.io) load_graph_from_sif_tuples() (in module corneto.io) load_json() (corneto.graph.Graph class method) M milp_carnival() (in module corneto.methods) module corneto.backend corneto.data corneto.data.util corneto.graph corneto.io corneto.methods MultiSampleFBA (class in corneto.methods) MultiSampleIMAT (class in corneto.methods) N name() (corneto.methods.BidirectionalPHONEMeS static method) (corneto.methods.PHONEMeS static method) (corneto.methods.signaling.CellNOptDAG static method) ne (corneto.graph.BaseGraph property) neighbors() (corneto.graph.BaseGraph method) NonZeroIndicator() (corneto.backend.Backend method) num_edges (corneto.graph.BaseGraph property) num_vertices (corneto.graph.BaseGraph property) nv (corneto.graph.BaseGraph property) O out_edges() (corneto.graph.BaseGraph method) P Parameter() (corneto.backend.Backend method) (corneto.backend.CvxpyBackend method) (corneto.backend.PicosBackend method) parse_cobra_model() (in module corneto.io) PHONEMeS (class in corneto.methods) PicosBackend (class in corneto.backend) plot() (corneto.graph.BaseGraph method) plot_cellnopt_fit() (in module corneto.methods.signaling) plot_cellnopt_model() (in module corneto.methods.signaling) plot_model() (in module corneto.ml) plot_values() (corneto.graph.BaseGraph method) predecessors() (corneto.graph.BaseGraph method) preferential_attachment_network() (in module corneto.graph) preprocess() (corneto.methods.BidirectionalPHONEMeS method) (corneto.methods.CarnivalFlow method) (corneto.methods.CarnivalILP method) (corneto.methods.MultiSampleFBA method) (corneto.methods.MultiSampleIMAT method) (corneto.methods.PHONEMeS method) (corneto.methods.PrizeCollectingSteinerTree method) (corneto.methods.signaling.CellNOptDAG method) PrizeCollectingSteinerTree (class in corneto.methods) Problem() (corneto.backend.Backend method) prune() (corneto.graph.BaseGraph method) Q query (corneto.data.Data property) (corneto.data.Sample property) R reachability_analysis() (corneto.graph.BaseGraph method) references() (corneto.methods.CarnivalFlow static method) (corneto.methods.CarnivalILP static method) (corneto.methods.MultiSampleFBA static method) (corneto.methods.MultiSampleIMAT static method) (corneto.methods.PHONEMeS static method) reverse() (corneto.graph.BaseGraph method) (corneto.graph.Graph method) S Sample (class in corneto.data) sample_alternative_solutions() (in module corneto.methods.sampler) samples (corneto.data.Data property) save() (corneto.data.Data method) (corneto.graph.BaseGraph method) save_json() (corneto.graph.Graph method) shape (corneto.graph.BaseGraph property) shortest_path() (in module corneto.methods) signed_dense() (in module corneto.ml) solve() (corneto.backend.Backend method) solve_shortest_path() (in module corneto.methods) SteinerTreeFlow (class in corneto.methods) subgraph() (corneto.graph.BaseGraph method) successors() (corneto.graph.BaseGraph method) T to_dict() (corneto.data.Data method) (corneto.data.Sample method) (corneto.graph.Graph method) to_dot() (corneto.graph.BaseGraph method) to_graphviz() (corneto.graph.BaseGraph method) to_json() (corneto.data.Data method) (corneto.graph.Graph method) toposort() (corneto.graph.BaseGraph method) (in module corneto.ml) U UNDIRECTED (corneto.graph.EdgeType attribute) V V (corneto.graph.BaseGraph property) Variable() (corneto.backend.Backend method) (corneto.backend.CvxpyBackend method) (corneto.backend.PicosBackend method) VarType (class in corneto.backend) version() (corneto.backend.Backend method) vertex_incidence_matrix() (corneto.graph.BaseGraph method) vertices (corneto.graph.BaseGraph property) vstack() (corneto.backend.Backend method) Z zero_function() (corneto.backend.Backend method)
