Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | X | Z _ __init__() (corneto.data.Data method) (corneto.data.Sample method) (corneto.graph.BaseGraph method) (corneto.graph.EdgeType method) (corneto.graph.Graph method) (corneto.methods.future.CarnivalFlow method) (corneto.methods.future.CarnivalILP method) (corneto.methods.future.MultiSampleFBA method) A Acyclic() (corneto.backend.Backend method) Acyclic0() (corneto.backend.Backend method) AcyclicFlow() (corneto.backend.Backend method) add_edge() (corneto.graph.BaseGraph method) add_edges() (corneto.graph.BaseGraph method) add_feature() (corneto.data.Sample method) add_sample() (corneto.data.Data method) add_vertex() (corneto.graph.BaseGraph method) add_vertices() (corneto.graph.BaseGraph method) available_solvers() (corneto.backend.Backend method) (corneto.backend.CvxpyBackend method) (corneto.backend.PicosBackend method) B Backend (class in corneto.backend) backend (corneto.methods.future.MultiSampleFBA attribute) BaseGraph (class in corneto.graph) beta_reg (corneto.methods.future.MultiSampleFBA attribute) bfs() (corneto.graph.BaseGraph method) BINARY (corneto.backend.VarType attribute) build() (corneto.backend.Backend method) (corneto.backend.CvxpyBackend method) (corneto.backend.PicosBackend method) C CarnivalFlow (class in corneto.methods.future) CarnivalILP (class in corneto.methods.future) cobra_model_to_graph() (in module corneto.io) collect_features() (corneto.data.Data method) 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.future module create_flow_based_problem() (corneto.methods.future.CarnivalFlow method) (corneto.methods.future.MultiSampleFBA method) create_problem() (corneto.methods.future.CarnivalILP method) CvxpyBackend (class in corneto.backend) D Data (class in corneto.data) data (corneto.data.Data attribute) delete_sample() (corneto.data.Data method) DIRECTED (corneto.graph.EdgeType attribute), [1] disable_structured_sparsity (corneto.methods.future.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) extract_subgraph() (corneto.graph.BaseGraph method) (corneto.graph.Graph method) F features (corneto.data.Sample attribute) filter() (corneto.data.Data method) (corneto.data.Sample method) filter_by() (corneto.data.Data method) (corneto.data.Sample method) filter_graph() (corneto.graph.Graph method) filter_samples() (corneto.data.Data method) filter_values() (corneto.data.Sample method) filter_values_by() (corneto.data.Sample method) Flow() (corneto.backend.Backend method) flux_indicator_name (corneto.methods.future.MultiSampleFBA attribute) from_dict() (corneto.data.Data class method) (corneto.graph.Graph class method) from_json() (corneto.graph.Graph class method) from_sample_value_dict() (corneto.data.Data class method) from_tight_format() (corneto.data.Data class method) from_tuples() (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_citations() (corneto.methods.future.CarnivalFlow static method) (corneto.methods.future.CarnivalILP static method) (corneto.methods.future.MultiSampleFBA static 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_feature_across_samples() (corneto.data.Data method) get_flow_bounds() (corneto.methods.future.MultiSampleFBA 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_value() (corneto.data.Sample method) get_values() (corneto.data.Sample 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) Indicator() (corneto.backend.Backend method) Indicators() (corneto.backend.Backend method) INTEGER (corneto.backend.VarType attribute) is_available() (corneto.backend.Backend method) is_hypergraph() (corneto.graph.BaseGraph method) L lambda_reg (corneto.methods.future.MultiSampleFBA attribute) linear_and() (corneto.backend.Backend method) linear_or() (corneto.backend.Backend method) linear_xor() (corneto.backend.Backend method) load() (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 merge() (corneto.data.Data method) module corneto.backend corneto.data corneto.data.util corneto.graph corneto.io corneto.methods.future MultiSampleFBA (class in corneto.methods.future) N 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) PicosBackend (class in corneto.backend) plot() (corneto.graph.BaseGraph method) plot_values() (corneto.graph.BaseGraph method) predecessors() (corneto.graph.BaseGraph method) preferential_attachment_network() (in module corneto.graph) preprocess() (corneto.methods.future.CarnivalFlow method) (corneto.methods.future.CarnivalILP method) (corneto.methods.future.MultiSampleFBA method) Problem() (corneto.backend.Backend method) prune() (corneto.graph.BaseGraph method) R reachability_analysis() (corneto.graph.BaseGraph method) reverse() (corneto.graph.BaseGraph method) (corneto.graph.Graph method) S Sample (class in corneto.data) save() (corneto.graph.BaseGraph method) save_json() (corneto.graph.Graph method) shape (corneto.graph.BaseGraph property) solve() (corneto.backend.Backend method) subgraph() (corneto.graph.BaseGraph method) subset_features() (corneto.data.Data method) successors() (corneto.graph.BaseGraph method) T to_dict() (corneto.graph.Graph method) to_dot() (corneto.graph.BaseGraph method) to_graphviz() (corneto.graph.BaseGraph method) to_json() (corneto.graph.Graph method) to_sample_value_dict() (corneto.data.Data method) to_tight_format() (corneto.data.Data method) toposort() (corneto.graph.BaseGraph method) U UNDIRECTED (corneto.graph.EdgeType attribute), [1] update_sample() (corneto.data.Data method) 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) X Xor() (corneto.backend.Backend method) Z zero_function() (corneto.backend.Backend method)
