Reference

• cellmaps_hierarchyeval package
  • Submodules
  • cellmaps_hierarchyeval.analysis module
    • Assembly
      • Assembly.get_assembly_name()
      • Assembly.get_gene_names()
      • Assembly.get_node_id()
      • Assembly.set_assembly_name()
    • FakeGeneSetAgent
      • FakeGeneSetAgent.annotate_gene_set()
    • GenesetAgent
      • GenesetAgent.GENE_SET_TOKEN
      • GenesetAgent.annotate_gene_set()
      • GenesetAgent.get_attribute_name_prefix()
    • Hierarchy
      • Hierarchy.get_next_assembly()
    • OllamaCommandLineGeneSetAgent
      • OllamaCommandLineGeneSetAgent.DEFAULT_PROMPT_FILE
      • OllamaCommandLineGeneSetAgent.annotate_gene_set()
      • OllamaCommandLineGeneSetAgent.get_default_prompt()
      • OllamaCommandLineGeneSetAgent.get_prompt()
    • OllamaRestServiceGenesetAgent
      • OllamaRestServiceGenesetAgent.annotate_gene_set()
      • OllamaRestServiceGenesetAgent.get_prompt()
  • cellmaps_hierarchyeval.perturb module
    • PerturbSeqAnalysis
      • PerturbSeqAnalysis.compare_cluster_root_similarities()
      • PerturbSeqAnalysis.get_cluster_similarity()
      • PerturbSeqAnalysis.get_heatmap_for_given_hierarchy_system()
      • PerturbSeqAnalysis.get_root_functional_data_similarity()
      • PerturbSeqAnalysis.get_root_gene_pair_similarities()
      • PerturbSeqAnalysis.get_root_overlapping_pair_similarities()
  • cellmaps_hierarchyeval.cellmaps_hierarchyevalcmd module
    • get_model_prompt_from_string()
    • get_ollama_geneset_agents()
    • main()
  • cellmaps_hierarchyeval.exceptions module
    • CellmapshierarchyevalError
  • cellmaps_hierarchyeval.runner module
    • BaseNetworkHelper
      • BaseNetworkHelper.get_hierarchy_input_file()
    • CORUM_EnrichmentTerms
    • CX2NetworkHelper
      • CX2NetworkHelper.dump_to_file()
      • CX2NetworkHelper.get_format()
      • CX2NetworkHelper.get_hierarchy()
      • CX2NetworkHelper.get_hierarchy_real_ids()
      • CX2NetworkHelper.get_node_genes()
      • CX2NetworkHelper.get_nodes()
      • CX2NetworkHelper.get_suffix()
      • CX2NetworkHelper.write_as_nodelist()
    • CellmapshierarchyevalRunner
      • CellmapshierarchyevalRunner.CORUM
      • CellmapshierarchyevalRunner.GO_CC
      • CellmapshierarchyevalRunner.HPA
      • CellmapshierarchyevalRunner.MAX_FDR
      • CellmapshierarchyevalRunner.MIN_COMP_SIZE
      • CellmapshierarchyevalRunner.MIN_JACCARD_INDEX
      • CellmapshierarchyevalRunner.NDEX_SERVER
      • CellmapshierarchyevalRunner.generate_readme()
      • CellmapshierarchyevalRunner.get_annotated_hierarchy_as_nodelist_dest_file()
      • CellmapshierarchyevalRunner.get_annotated_hierarchy_dest_file()
      • CellmapshierarchyevalRunner.get_hierarchy_parent_network_dest_file()
      • CellmapshierarchyevalRunner.initialize_hierarchy_helper()
      • CellmapshierarchyevalRunner.run()
    • EnrichmentResult
      • EnrichmentResult.set_accepted()
      • EnrichmentResult.set_adjusted_pval()
      • EnrichmentResult.set_description()
    • EnrichmentTerms
    • GO_EnrichmentTerms
    • GeneSetAgentAnnotator
      • GeneSetAgentAnnotator.annotate_hierarchy()
      • GeneSetAgentAnnotator.set_hierarchy_helper()
      • GeneSetAgentAnnotator.set_minimum_comparison_size()
    • HPA_EnrichmentTerms
    • HiDeF_EnrichmentTerms
    • NiceCXNetworkHelper
      • NiceCXNetworkHelper.dump_to_file()
      • NiceCXNetworkHelper.get_format()
      • NiceCXNetworkHelper.get_hierarchy()
      • NiceCXNetworkHelper.get_hierarchy_real_ids()
      • NiceCXNetworkHelper.get_node_genes()
      • NiceCXNetworkHelper.get_nodes()
      • NiceCXNetworkHelper.get_suffix()
      • NiceCXNetworkHelper.write_as_nodelist()
  • Module contents