INDRA CoGEx 1.0.0 Documentation

Getting Started

• License and funding
• Enrichment and Set Analysis
  • Discrete GSEA
    • Form Fields
  • Signed GSEA
    • Form Fields
  • Continuous GSEA
    • Form Fields
  • Discrete MSEA
    • Form Fields
• INDRA CoGEx modules reference
  • INDRA CoGEx Knowledge Assembly (indra_cogex.assembly)
    • NodeAssembler
  • INDRA CoGEx Client
    • Enrichment Analysis (indra_cogex.client.enrichment)
    • Neo4j Client (indra_cogex.client.neo4j_client)
    • The INDRA CoGEx Neo4j Client (indra_cogex.client.queries)
    • Subnetwork Client (indra_cogex.client.subnetwork)
  • Indexing of The Database
    • Indexing The Database (indra_cogex.indexing)
    • Indexing CLI (indra_cogex.indexing.cli)
  • INDRA CoGEx Sources
    • Source CLI (indra_cogex.sources.cli)
    • INDRA CoGEx Sources Processor (indra_cogex.sources.processor)
    • Data Validation (indra_cogex.sources.processor_util)
    • Bgee Processor (indra_cogex.sources.bgee)
    • cBioPortal Processor (indra_cogex.sources.cbioportal)
    • CellMarker Processor (indra_cogex.sources.cellmarker)
    • chembl Processor (indra_cogex.sources.chembl)
    • clinicaltrials Processor (indra_cogex.sources.clinicaltrials)
    • DisGeNet Processor (indra_cogex.sources.disgenet)
    • HGNCEnzyme Processor (indra_cogex.sources.ec)
    • goa Processor (indra_cogex.sources.goa)
    • GWAS Processor (indra_cogex.sources.gwas)
    • HPOA Processor (indra_cogex.sources.hpoa)
    • INDRA DB Processor (indra_cogex.sources.indra_db)
    • INDRA Ontology Processor (indra_cogex.sources.indra_ontology)
    • InterPro Processor (indra_cogex.sources.interpro)
    • NIH RePORTER Processor (indra_cogex.sources.nih_reporter)
    • Odinson Processor (indra_cogex.sources.odinson)
    • Pathways Processor (indra_cogex.sources.pathways)
    • PubMed Processor (indra_cogex.sources.pubmed)
    • Sider Processor (indra_cogex.sources.sider)
    • WikiData Processor (indra_cogex.sources.wikidata)
  • INDRA CoGEx Representation (indra_cogex.representation)
    • Node
    • Relation
    • indra_stmts_from_relations()
    • norm_id()

Indices and Tables

• Index

• Module Index

• Search Page