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API Reference

NeKo's public API is organised into five main areas:

Module Description
neko.core.network.Network Core class – build, manipulate, and query a signalling network
neko._visual.visualize_network.NetworkVisualizer Render networks with Graphviz or the yFiles widget
neko._methods.enrichment_methods.Connections Algorithms for enriching a network from an interaction database
neko._annotations.gene_ontology.Ontology Gene Ontology utilities and phenotype mapping
neko._outputs.exports Export helpers (SIF, GML, GraphML, BND/CFG)

Design philosophy

NeKo follows a Network-centric design:

  1. Start with a list of gene/protein identifiers.
  2. Attach an interaction Universe from OmniPath (or custom CSV/DataFrame).
  3. Use Network methods to connect, expand, and annotate nodes.
  4. Visualise or export the result.

All mutation methods on Network automatically create a snapshot in the branching NetworkHistory, so every intermediate state is recoverable.

Import conventions

# Core
from neko.core.network import Network

# Visualisation
from neko._visual.visualize_network import NetworkVisualizer

# Interaction universe
from neko.inputs import Universe

# Ontology
from neko._annotations.gene_ontology import Ontology