API

Import Neko as:

from neko.core.network import Network

Network

neko.core.network.Network.load_network_from_sif(...)

Load a network object from a SIF (Simple Interaction Format) file.

neko.core.network.Network.add_edge(edge)

This method adds an interaction to the list of interactions while converting it to the Omniflow-network format.

neko.core.network.Network.remove_node(node)

Removes a node from the network.

neko.core.network.Network.add_cascade_to_edge_list(...)

This function adds cascades to the edge list of the network.

neko.core.network.Network.add_node(node)

Adds a node to the network.

neko.core.network.Network.add_paths_to_edge_list(paths)

This method adds paths to the edge list of the network.

neko.core.network.Network.complete_connection([...])

This function attempts to connect all nodes of a network object using one of the methods presented in the Connection object.

neko.core.network.Network.connect_component(...)

This function attempts to connect subcomponents of a network object using one of the methods presented in the Connection object.

neko.core.network.Network.connect_genes_to_phenotype([...])

This function connects genes to a phenotype based on the provided parameters.

neko.core.network.Network.connect_nodes([...])

Basic node connections.

neko.core.network.Network.connect_subgroup(group)

This function is used to connect all the nodes in a particular subgroup.

neko.core.network.Network.connect_to_upstream_nodes([...])

Connects to upstream nodes based on the provided parameters.

neko.core.network.Network.convert_edgelist_into_genesymbol()

This function converts the edge dataframe from uniprot to genesymbol.

neko.core.network.Network.filter_unsigned_paths(...)

This function filters out unsigned paths from the provided list of paths.

neko.core.network.Network.is_connected()

Return True if all the nodes in the nodes list in the Network object are connected, otherwise it returns False