Index

A

abc2cas() (in module cas.abc_cas_converter) add_annotation_object() (cas.model.CellTypeAnnotation method) add_annotations() (in module cas.abc_cas_converter) add_annotations_to_cas() (in module cas.anndata_to_cas) (in module cas.spreadsheet_to_cas) add_author_annotations() (in module cas.add_author_annotations) add_author_annotations_from_file() (in module cas.add_author_annotations) add_cell_ids() (in module cas.populate_cell_ids) add_labelsets() (in module cas.abc_cas_converter) add_labelsets_to_cas() (in module cas.utils.conversion_utils) add_parent_cell_hierarchy() (in module cas.utils.conversion_utils) add_parent_hierarchy_to_annotations() (in module cas.utils.conversion_utils) add_parent_node_names() (in module cas.ingest.ingest_user_table) add_user_annotation() (cas.model.Annotation method) add_user_annotations() (in module cas.ingest.ingest_user_table) algorithm_name (cas.model.AnnotationTransfer attribute) (cas.model.AutomatedAnnotation attribute)

algorithm_repo_url (cas.model.AutomatedAnnotation attribute) algorithm_version (cas.model.AutomatedAnnotation attribute) anndata2cas() (in module cas.anndata_to_cas) Annotation (class in cas.model) annotation_method (cas.model.Labelset attribute) annotations (cas.model.CellTypeAnnotation attribute) AnnotationTransfer (class in cas.model) as_dictionary() (cas.model.CellTypeAnnotation method) assign_parent_accession_ids() (in module cas.flatten_data_to_tables) assign_parent_cell_set_names() (in module cas.flatten_data_to_tables) author_annotation_fields (cas.model.Annotation attribute) author_contact (cas.model.CellTypeAnnotation attribute) author_list (cas.model.CellTypeAnnotation attribute) author_name (cas.model.CellTypeAnnotation attribute) automated_annotation (cas.model.Labelset attribute) AutomatedAnnotation (class in cas.model)

B

BaseAccessionManager (class in cas.accession.base_accession_manager)

BaseMatrixFileResolver (class in cas.matrix_file.base_resolver)

C

calculate_labelset() (in module cas.utils.conversion_utils) calculate_labelset_rank() (in module cas.utils.conversion_utils) calculate_order_mapping() (in module cas.abc_cas_converter) cas module cas.abc_cas_converter module cas.accession module cas.accession.base_accession_manager module cas.accession.hash_accession_manager module cas.accession.incremental_accession_manager module cas.add_author_annotations module cas.anndata_conversion module cas.anndata_splitter module cas.anndata_to_cas module cas.cas_splitter module cas.cas_to_rdf module cas.cxg_utils module cas.file_utils module cas.flatten_data_to_anndata module cas.flatten_data_to_tables module cas.ingest module cas.ingest.config_validator module cas.ingest.ingest_user_table module cas.matrix_file module cas.matrix_file.base_resolver module

cas.matrix_file.cxg_resolver module cas.matrix_file.resolver module cas.model module cas.populate_cell_ids module cas.reports module cas.spreadsheet_to_cas module cas.utils module cas.utils.conversion_utils module cas.utils.validation_utils module cas.validate module cas2abc() (in module cas.abc_cas_converter) cell_fullname (cas.model.Annotation attribute) cell_ids (cas.model.Annotation attribute) cell_label (cas.model.Annotation attribute) cell_ontology_term (cas.model.Annotation attribute) cell_ontology_term_id (cas.model.Annotation attribute) cell_set_accession (cas.model.Annotation attribute) cellannotation_schema_version (cas.model.CellTypeAnnotation attribute) cellannotation_timestamp (cas.model.CellTypeAnnotation attribute) cellannotation_url (cas.model.CellTypeAnnotation attribute) cellannotation_version (cas.model.CellTypeAnnotation attribute) CellTypeAnnotation (class in cas.model) check_labelsets() (in module cas.anndata_conversion) check_parent_child_consistency() (in module cas.utils.validation_utils) collect_parent_cell_ids() (in module cas.utils.conversion_utils) comment (cas.model.AnnotationTransfer attribute) compare_labelsets_cas_obs() (in module cas.utils.validation_utils) convert_complex_type() (in module cas.utils.conversion_utils) copy_and_update_file_path() (in module cas.utils.conversion_utils) create_accession_mapping() (in module cas.utils.conversion_utils) create_cell_label_lookup() (in module cas.flatten_data_to_anndata) custom_lowercase_transform() (in module cas.spreadsheet_to_cas) CxGDatasetResolver (class in cas.matrix_file.cxg_resolver)

D

dataclass_json_config (cas.model.EncoderMixin attribute) dataframe_to_dict() (in module cas.add_author_annotations) datestamp (cas.model.Review attribute)

description (cas.model.CellTypeAnnotation attribute) (cas.model.Labelset attribute) download_dataset_with_id() (in module cas.cxg_utils)

E

EncoderMixin (class in cas.model) explanation (cas.model.Review attribute)

export2cap() (in module cas.flatten_data_to_anndata) export_cas_object2cap() (in module cas.flatten_data_to_anndata) export_to_rdf() (in module cas.cas_to_rdf)

F

fetch_anndata() (in module cas.utils.conversion_utils)

filter_and_copy_cas_entries() (in module cas.cas_splitter) filter_by_label() (in module cas.reports)

G

generate_accession_id() (cas.accession.base_accession_manager.BaseAccessionManager method) (cas.accession.hash_accession_manager.HashAccessionManager method) (cas.accession.incremental_accession_manager.IncrementalAccessionManager method) generate_annotation_table() (in module cas.flatten_data_to_tables) generate_annotation_transfer_table() (in module cas.flatten_data_to_tables) generate_cas_json() (in module cas.flatten_data_to_anndata) generate_cas_metadata() (in module cas.anndata_to_cas) generate_cat_dataframe() (in module cas.abc_cas_converter) generate_catset_dataframe() (in module cas.abc_cas_converter) generate_ids_for_annotations() (in module cas.ingest.ingest_user_table) generate_labelset_table() (in module cas.flatten_data_to_tables) generate_metadata_table() (in module cas.flatten_data_to_tables) generate_parent_cell_lookup() (in module cas.utils.conversion_utils)

generate_reviews_table() (in module cas.flatten_data_to_tables) generate_uns_json() (in module cas.flatten_data_to_anndata) get_all_annotations() (cas.model.CellTypeAnnotation method) (in module cas.reports) get_annotation() (in module cas.ingest.ingest_user_table) get_authors_from_doi() (in module cas.utils.conversion_utils) get_cas_schema() (in module cas.file_utils) get_cas_schema_names() (in module cas.file_utils) get_cell_ids() (in module cas.utils.conversion_utils) get_cl_annotations_from_anndata() (in module cas.utils.conversion_utils) get_matching_obs_keys() (in module cas.anndata_conversion) get_obs_cluster_identifier_column() (in module cas.populate_cell_ids) get_split_terms() (in module cas.cas_splitter)

H

handle_matching_labelset() (in module cas.anndata_conversion)

handle_non_matching_labelset() (in module cas.anndata_conversion) HashAccessionManager (class in cas.accession.hash_accession_manager)

I

IncrementalAccessionManager (class in cas.accession.incremental_accession_manager) infer_cas_cell_hierarchy() (in module cas.utils.validation_utils) infer_obs_cell_hierarchy() (in module cas.utils.validation_utils) ingest_data() (in module cas.ingest.ingest_user_table) ingest_user_data() (in module cas.ingest.ingest_user_table)

init_accession_managers() (in module cas.ingest.ingest_user_table) init_metadata() (in module cas.abc_cas_converter) initialize_cas_structure() (in module cas.spreadsheet_to_cas) is_hash_accession() (in module cas.accession.hash_accession_manager) is_list_of_strings() (in module cas.flatten_data_to_anndata)

L

labelset (cas.model.Annotation attribute) Labelset (class in cas.model) labelsets (cas.model.CellTypeAnnotation attribute)

list_cached_datasets() (in module cas.matrix_file.cxg_resolver) list_to_string() (in module cas.flatten_data_to_tables) load_or_fetch_anndata() (in module cas.spreadsheet_to_cas)

M

marker_gene_evidence (cas.model.Annotation attribute) matrix_file_id (cas.model.CellTypeAnnotation attribute) merge() (in module cas.anndata_conversion) merge_cas_object() (in module cas.anndata_conversion) module cas cas.abc_cas_converter cas.accession cas.accession.base_accession_manager cas.accession.hash_accession_manager cas.accession.incremental_accession_manager cas.add_author_annotations cas.anndata_conversion cas.anndata_splitter cas.anndata_to_cas cas.cas_splitter cas.cas_to_rdf cas.cxg_utils cas.file_utils cas.flatten_data_to_anndata cas.flatten_data_to_tables cas.ingest cas.ingest.config_validator cas.ingest.ingest_user_table cas.matrix_file cas.matrix_file.base_resolver cas.matrix_file.cxg_resolver cas.matrix_file.resolver cas.model cas.populate_cell_ids cas.reports cas.spreadsheet_to_cas cas.utils cas.utils.conversion_utils cas.utils.validation_utils cas.validate

N

name (cas.model.Labelset attribute) neurotransmitter_accession (cas.model.Annotation attribute)

neurotransmitter_marker_gene_evidence (cas.model.Annotation attribute) neurotransmitter_rationale (cas.model.Annotation attribute) normalize_column_name() (in module cas.flatten_data_to_tables)

O

orcid (cas.model.CellTypeAnnotation attribute)

P

parent_cell_set_accession (cas.model.Annotation attribute) parent_cell_set_name (cas.model.Annotation attribute)

populate_cell_ids() (in module cas.populate_cell_ids) populate_labelsets() (in module cas.ingest.ingest_user_table) process_annotations() (in module cas.flatten_data_to_anndata)

R

rank (cas.model.Labelset attribute) rationale (cas.model.Annotation attribute) rationale_dois (cas.model.Annotation attribute) read_anndata_file() (in module cas.file_utils) read_cas_from_anndata() (in module cas.file_utils) read_cas_json_file() (in module cas.file_utils) read_config() (in module cas.file_utils) read_csv_to_dict() (in module cas.file_utils) read_json_config() (in module cas.file_utils) read_json_file() (in module cas.file_utils) read_spreadsheet() (in module cas.spreadsheet_to_cas) read_table_to_dict() (in module cas.file_utils) read_tsv_to_dict() (in module cas.file_utils) read_yaml_config() (in module cas.file_utils) reference_location (cas.model.AutomatedAnnotation attribute)

reformat_json() (in module cas.utils.conversion_utils) register_parent() (in module cas.ingest.ingest_user_table) remove_none_values() (cas.model.CellTypeAnnotation method) resolve_matrix_file() (cas.matrix_file.base_resolver.BaseMatrixFileResolver method) (cas.matrix_file.cxg_resolver.CxGDatasetResolver method) (in module cas.matrix_file.resolver) resolve_matrix_file_path() (cas.matrix_file.base_resolver.BaseMatrixFileResolver method) (cas.matrix_file.cxg_resolver.CxGDatasetResolver method) (in module cas.matrix_file.resolver) resolve_ref() (in module cas.spreadsheet_to_cas) retrieve_schema() (in module cas.utils.conversion_utils) review (cas.model.Review attribute) Review (class in cas.model) reviewer (cas.model.Review attribute) reviews (cas.model.Annotation attribute)

S

serialize_to_tables() (in module cas.flatten_data_to_tables) set_exclude_none_values() (cas.model.CellTypeAnnotation method) source_node_accession (cas.model.AnnotationTransfer attribute) source_taxonomy (cas.model.AnnotationTransfer attribute) split_anndata() (in module cas.anndata_splitter)

split_anndata_to_file() (in module cas.anndata_splitter) split_cas() (in module cas.cas_splitter) split_cas_to_file() (in module cas.cas_splitter) spreadsheet2cas() (in module cas.spreadsheet_to_cas) synonyms (cas.model.Annotation attribute)

T

test_compatibility() (in module cas.anndata_conversion) title (cas.model.CellTypeAnnotation attribute)

transferred_annotations (cas.model.Annotation attribute) transferred_cell_label (cas.model.AnnotationTransfer attribute)

U

unflatten() (in module cas.flatten_data_to_anndata) unflatten_obs() (in module cas.flatten_data_to_anndata) update_cas_annotation() (in module cas.flatten_data_to_anndata)

update_cas_with_cell_ids() (in module cas.populate_cell_ids) update_obs() (in module cas.file_utils) update_parent_info() (in module cas.utils.conversion_utils) update_uns() (in module cas.file_utils)

V

validate() (in module cas.ingest.config_validator) (in module cas.validate) validate_cell_ids() (in module cas.anndata_conversion) validate_columns() (in module cas.add_author_annotations) validate_dataframe_columns() (in module cas.abc_cas_converter) validate_file() (in module cas.ingest.config_validator)

validate_json_str() (in module cas.ingest.config_validator) validate_labelset_hierarchy() (in module cas.utils.validation_utils) validate_labelset_markers() (in module cas.utils.validation_utils) validate_labelset_values() (in module cas.utils.validation_utils) validate_markers() (in module cas.utils.validation_utils) validate_values() (in module cas.add_author_annotations)

W

write_dict_to_json_file() (in module cas.file_utils)

write_json_file() (in module cas.file_utils)