Index

A

annotate_gene_set() (cellmaps_hierarchyeval.analysis.FakeGeneSetAgent method) (cellmaps_hierarchyeval.analysis.GenesetAgent method) (cellmaps_hierarchyeval.analysis.OllamaCommandLineGeneSetAgent method) (cellmaps_hierarchyeval.analysis.OllamaRestServiceGenesetAgent method)

annotate_hierarchy() (cellmaps_hierarchyeval.runner.GeneSetAgentAnnotator method) Assembly (class in cellmaps_hierarchyeval.analysis)

B

BaseNetworkHelper (class in cellmaps_hierarchyeval.runner)

C

cellmaps_hierarchyeval module cellmaps_hierarchyeval.analysis module cellmaps_hierarchyeval.cellmaps_hierarchyevalcmd module cellmaps_hierarchyeval.exceptions module cellmaps_hierarchyeval.perturb module

cellmaps_hierarchyeval.runner module CellmapshierarchyevalError CellmapshierarchyevalRunner (class in cellmaps_hierarchyeval.runner) compare_cluster_root_similarities() (cellmaps_hierarchyeval.perturb.PerturbSeqAnalysis static method) CORUM (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner attribute) CORUM_EnrichmentTerms (class in cellmaps_hierarchyeval.runner) CX2NetworkHelper (class in cellmaps_hierarchyeval.runner)

D

DEFAULT_PROMPT_FILE (cellmaps_hierarchyeval.analysis.OllamaCommandLineGeneSetAgent attribute)

dump_to_file() (cellmaps_hierarchyeval.runner.CX2NetworkHelper static method) (cellmaps_hierarchyeval.runner.NiceCXNetworkHelper static method)

E

EnrichmentResult (class in cellmaps_hierarchyeval.runner)

EnrichmentTerms (class in cellmaps_hierarchyeval.runner)

F

FakeGeneSetAgent (class in cellmaps_hierarchyeval.analysis)

G

GENE_SET_TOKEN (cellmaps_hierarchyeval.analysis.GenesetAgent attribute) generate_readme() (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner method) GenesetAgent (class in cellmaps_hierarchyeval.analysis) GeneSetAgentAnnotator (class in cellmaps_hierarchyeval.runner) get_annotated_hierarchy_as_nodelist_dest_file() (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner method) get_annotated_hierarchy_dest_file() (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner method) get_assembly_name() (cellmaps_hierarchyeval.analysis.Assembly method) get_attribute_name_prefix() (cellmaps_hierarchyeval.analysis.GenesetAgent method) get_cluster_similarity() (cellmaps_hierarchyeval.perturb.PerturbSeqAnalysis method) get_default_prompt() (cellmaps_hierarchyeval.analysis.OllamaCommandLineGeneSetAgent static method) get_format() (cellmaps_hierarchyeval.runner.CX2NetworkHelper static method) (cellmaps_hierarchyeval.runner.NiceCXNetworkHelper static method) get_gene_names() (cellmaps_hierarchyeval.analysis.Assembly method) get_heatmap_for_given_hierarchy_system() (cellmaps_hierarchyeval.perturb.PerturbSeqAnalysis method) get_hierarchy() (cellmaps_hierarchyeval.runner.CX2NetworkHelper method) (cellmaps_hierarchyeval.runner.NiceCXNetworkHelper method) get_hierarchy_input_file() (cellmaps_hierarchyeval.runner.BaseNetworkHelper method) get_hierarchy_parent_network_dest_file() (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner method)

get_hierarchy_real_ids() (cellmaps_hierarchyeval.runner.CX2NetworkHelper static method) (cellmaps_hierarchyeval.runner.NiceCXNetworkHelper static method) get_model_prompt_from_string() (in module cellmaps_hierarchyeval.cellmaps_hierarchyevalcmd) get_next_assembly() (cellmaps_hierarchyeval.analysis.Hierarchy method) get_node_genes() (cellmaps_hierarchyeval.runner.CX2NetworkHelper static method) (cellmaps_hierarchyeval.runner.NiceCXNetworkHelper static method) get_node_id() (cellmaps_hierarchyeval.analysis.Assembly method) get_nodes() (cellmaps_hierarchyeval.runner.CX2NetworkHelper static method) (cellmaps_hierarchyeval.runner.NiceCXNetworkHelper static method) get_ollama_geneset_agents() (in module cellmaps_hierarchyeval.cellmaps_hierarchyevalcmd) get_prompt() (cellmaps_hierarchyeval.analysis.OllamaCommandLineGeneSetAgent method) (cellmaps_hierarchyeval.analysis.OllamaRestServiceGenesetAgent method) get_root_functional_data_similarity() (cellmaps_hierarchyeval.perturb.PerturbSeqAnalysis static method) get_root_gene_pair_similarities() (cellmaps_hierarchyeval.perturb.PerturbSeqAnalysis method) get_root_overlapping_pair_similarities() (cellmaps_hierarchyeval.perturb.PerturbSeqAnalysis static method) get_suffix() (cellmaps_hierarchyeval.runner.CX2NetworkHelper static method) (cellmaps_hierarchyeval.runner.NiceCXNetworkHelper static method) GO_CC (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner attribute) GO_EnrichmentTerms (class in cellmaps_hierarchyeval.runner)

H

HiDeF_EnrichmentTerms (class in cellmaps_hierarchyeval.runner) Hierarchy (class in cellmaps_hierarchyeval.analysis)

HPA (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner attribute) HPA_EnrichmentTerms (class in cellmaps_hierarchyeval.runner)

I

initialize_hierarchy_helper() (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner method)

M

main() (in module cellmaps_hierarchyeval.cellmaps_hierarchyevalcmd) MAX_FDR (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner attribute) MIN_COMP_SIZE (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner attribute) MIN_JACCARD_INDEX (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner attribute) module cellmaps_hierarchyeval cellmaps_hierarchyeval.analysis cellmaps_hierarchyeval.cellmaps_hierarchyevalcmd cellmaps_hierarchyeval.exceptions cellmaps_hierarchyeval.perturb cellmaps_hierarchyeval.runner

N

NDEX_SERVER (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner attribute)

NiceCXNetworkHelper (class in cellmaps_hierarchyeval.runner)

O

OllamaCommandLineGeneSetAgent (class in cellmaps_hierarchyeval.analysis)

OllamaRestServiceGenesetAgent (class in cellmaps_hierarchyeval.analysis)

P

PerturbSeqAnalysis (class in cellmaps_hierarchyeval.perturb)

R

run() (cellmaps_hierarchyeval.runner.CellmapshierarchyevalRunner method)

S

set_accepted() (cellmaps_hierarchyeval.runner.EnrichmentResult method) set_adjusted_pval() (cellmaps_hierarchyeval.runner.EnrichmentResult method) set_assembly_name() (cellmaps_hierarchyeval.analysis.Assembly method)

set_description() (cellmaps_hierarchyeval.runner.EnrichmentResult method) set_hierarchy_helper() (cellmaps_hierarchyeval.runner.GeneSetAgentAnnotator method) set_minimum_comparison_size() (cellmaps_hierarchyeval.runner.GeneSetAgentAnnotator method)

W

write_as_nodelist() (cellmaps_hierarchyeval.runner.CX2NetworkHelper static method) (cellmaps_hierarchyeval.runner.NiceCXNetworkHelper static method)