Index

_

_anndata (pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer attribute)

A

add_metadata_nodes() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method) add_outgoing_edges_to_subgraph() (in module pandasaurus_cxg.graph_generator.graph_generator_utils) all_cell_type_identifiers (pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer attribute) AnndataAnalyzer (class in pandasaurus_cxg.anndata_analyzer)

AnndataEnricher (class in pandasaurus_cxg.anndata_enricher) AnndataEnrichmentAnalyzer (class in pandasaurus_cxg.enrichment_analysis) AnndataLoader (class in pandasaurus_cxg.utils.anndata_loader) annotate_anndata_with_cell_type() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method) (pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)

C

CellTypeNotFoundError check_subclass_relationships() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method) co_annotation_report() (pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer method) (pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)

contextual_slim_enrichment() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method) (pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method) create_cell_type_dict() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)

E

enrich_rdf_graph() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method)

enriched_co_annotation_report() (pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer method) (pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)

F

filter_anndata_with_enriched_cell_type() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method) (pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method) find_and_rotate_center_layout() (in module pandasaurus_cxg.graph_generator.graph_generator_utils)

from_file_path() (pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer static method) (pandasaurus_cxg.anndata_enricher.AnndataEnricher static method) full_slim_enrichment() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method) (pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)

G

generate_rdf_graph() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method)

get_cxg_dataset_url() (in module pandasaurus_cxg.graph_generator.graph_generator_utils) GraphGenerator (class in pandasaurus_cxg.graph_generator.graph_generator)

I

InvalidGraphFormat

InvalidSlimName

L

load_from_file() (pandasaurus_cxg.utils.anndata_loader.AnndataLoader static method)

M

minimal_slim_enrichment() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method) (pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method) MissingAnalysisProcess

MissingEnrichmentProcess module pandasaurus_cxg.graph_generator.graph_generator_utils pandasaurus_cxg.utils.exceptions

P

pandasaurus_cxg.graph_generator.graph_generator_utils module

pandasaurus_cxg.utils.exceptions module parse_citation_field_into_dict() (in module pandasaurus_cxg.graph_generator.graph_generator_utils)

S

save_rdf_graph() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method) set_enricher_property_list() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method) set_label_adding_priority() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method)

simple_enrichment() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method) (pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method) SubclassWarning

V

validate_slim_list() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)

visualize_rdf_graph() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method)