LiPI

Lipid Pathway Integrator

• Unifies lipid ontology-aware representation and pathway-based multi-omics integration in a single framework

• Ingests existing reference pathways from KEGG and supports defining custom pathways via YAML

• Pathways are represented as editable graph-structured data specifically designed to accommodate individual molecular lipid species

• Feature-level statistics from any -omics data type can be mapped to pathway nodes and visualized to support interpretation

Contents:

• API Reference
  • lipi
    • lipi.identifiers
      • Identifier
        • Identifier.name
        • Identifier.tags
        • Identifier.from_kwargs()
      • IdentifierGroup
        • IdentifierGroup.name
        • IdentifierGroup.components
        • IdentifierGroup.entity_id
        • IdentifierGroup.components
        • IdentifierGroup.name
        • IdentifierGroup.entity_id
        • IdentifierGroup.size
        • IdentifierGroup.from_name()
        • IdentifierGroup.contains()
      • lipi.identifiers.ingestion
        • lipi.identifiers.ingestion.lipid_maps
          • ingest_lipid_maps_classes()
    • lipi.mapping
      • map_omics_data_to_pathway()
    • lipi.network
      • load_pathway()
      • lipi.network.nodes
        • Metabolite
        • Protein
          • Protein.igroup
          • Protein.stats
        • Lipid
          • Lipid.igroup
          • Lipid.stats
          • Lipid.fas
          • Lipid.fa_carbon
          • Lipid.fa_unsat
          • Lipid.fas
        • LipidGroup
          • LipidGroup.name
          • LipidGroup.lm_category
          • LipidGroup.lm_class
          • LipidGroup.lm_subclass
          • LipidGroup.lipids
          • LipidGroup.require_fas
          • LipidGroup.exclude_fas
          • LipidGroup.exact_fas
          • LipidGroup.igroup
          • LipidGroup.lm_category
          • LipidGroup.lm_class
          • LipidGroup.lm_subclass
          • LipidGroup.lipids
          • LipidGroup.require_fas
          • LipidGroup.exclude_fas
          • LipidGroup.exact_fas
          • LipidGroup.find_filtered_lipid_stats_with_tags()
    • lipi.refpath
      • lipi.refpath.manager
        • RefPathManager
          • RefPathManager.db_path
          • RefPathManager.connected
          • RefPathManager.create()
          • RefPathManager.db_path
          • RefPathManager.connected
          • RefPathManager.get_read_only_connection()
          • RefPathManager.commit()
          • RefPathManager.close()
          • RefPathManager.reconnect()
    • lipi.stats
      • Statistic
        • Statistic.value
        • Statistic.tags
        • Statistic.from_kwargs()
        • Statistic.add_tags()
      • load_stats_from_csv()
    • lipi.translation
      • lipi.translation.kegg
        • ingest_kegg_pathway()
      • lipi.translation.yaml
        • ingest_yaml_pathway()
    • lipi.visualization
      • plot_pathway_layout()
      • plot_pathway_stats()

Indices and tables

• Index

• Module Index

• Search Page