Index

A

ALL_CELLS (cellarium.cas.postprocessing.ontology_aware.CellOntologyScoresAggregationDomain attribute) allowed_models_list (cellarium.cas.client.CASClient property) annotate_10x_h5_file() (cellarium.cas.client.CASClient method) annotate_anndata() (cellarium.cas.client.CASClient method) annotate_anndata_file() (cellarium.cas.client.CASClient method)

annotate_matrix_cell_type_ontology_aware_strategy() (cellarium.cas.client.CASClient method) annotate_matrix_cell_type_summary_statistics_strategy() (cellarium.cas.client.CASClient method) ASSAY (cellarium.cas.constants.CellMetadataFeatures attribute) assay (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) ASSAY_ONTOLOGY_TERM_ID (cellarium.cas.constants.CellMetadataFeatures attribute) assay_ontology_term_id (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute)

C

CAS_CELL_INDEX (cellarium.cas.constants.CellMetadataFeatures attribute) cas_cell_index (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) (cellarium.cas.models.MatrixQueryResults.Match attribute) CASCircularTreePlotUMAPDashApp (class in cellarium.cas.visualization) CASClient (class in cellarium.cas.client) cell_count (cellarium.cas.models.CellTypeSummaryStatisticsResults.SummaryStatistics attribute) CELL_TYPE (cellarium.cas.constants.CellMetadataFeatures attribute) cell_type (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) (cellarium.cas.models.CellTypeOntologyAwareResults.Match attribute) (cellarium.cas.models.CellTypeSummaryStatisticsResults.SummaryStatistics attribute)

CELL_TYPE_ONTOLOGY_TERM_ID (cellarium.cas.constants.CellMetadataFeatures attribute) cell_type_ontology_term_id (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) (cellarium.cas.models.CellTypeOntologyAwareResults.Match attribute) cellarium.cas.client module CellMetadataFeatures (class in cellarium.cas.constants) CellOntologyScoresAggregationDomain (class in cellarium.cas.postprocessing.ontology_aware) CellOntologyScoresAggregationOp (class in cellarium.cas.postprocessing.ontology_aware) count_per_dataset (cellarium.cas.models.CellTypeSummaryStatisticsResults.DatasetStatistics attribute) CountMatrixInput (class in cellarium.cas.constants)

D

data (cellarium.cas.models.CellQueryResults attribute) (cellarium.cas.models.CellTypeOntologyAwareResults attribute) (cellarium.cas.models.CellTypeSummaryStatisticsResults attribute) (cellarium.cas.models.MatrixQueryResults attribute) dataset_id (cellarium.cas.models.CellTypeSummaryStatisticsResults.DatasetStatistics attribute) dataset_ids_with_counts (cellarium.cas.models.CellTypeSummaryStatisticsResults.SummaryStatistics attribute) DEVELOPMENT_STAGE (cellarium.cas.constants.CellMetadataFeatures attribute) development_stage (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute)

DEVELOPMENT_STAGE_ONTOLOGY_TERM_ID (cellarium.cas.constants.CellMetadataFeatures attribute) development_stage_ontology_term_id (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) DISEASE (cellarium.cas.constants.CellMetadataFeatures attribute) disease (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) DISEASE_ONTOLOGY_TERM_ID (cellarium.cas.constants.CellMetadataFeatures attribute) disease_ontology_term_id (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) distance (cellarium.cas.models.MatrixQueryResults.Match attribute) DONOR_ID (cellarium.cas.constants.CellMetadataFeatures attribute) donor_id (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute)

I

IS_PRIMARY_DATA (cellarium.cas.constants.CellMetadataFeatures attribute)

is_primary_data (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute)

M

matches (cellarium.cas.models.CellTypeOntologyAwareResults.OntologyAwareAnnotation attribute) (cellarium.cas.models.CellTypeSummaryStatisticsResults.NeighborhoodAnnotation attribute) max_distance (cellarium.cas.models.CellTypeSummaryStatisticsResults.DatasetStatistics attribute) (cellarium.cas.models.CellTypeSummaryStatisticsResults.SummaryStatistics attribute) MEAN (cellarium.cas.postprocessing.ontology_aware.CellOntologyScoresAggregationOp attribute) mean_distance (cellarium.cas.models.CellTypeSummaryStatisticsResults.DatasetStatistics attribute)

MEDIAN (cellarium.cas.postprocessing.ontology_aware.CellOntologyScoresAggregationOp attribute) median_distance (cellarium.cas.models.CellTypeSummaryStatisticsResults.DatasetStatistics attribute) (cellarium.cas.models.CellTypeSummaryStatisticsResults.SummaryStatistics attribute) min_distance (cellarium.cas.models.CellTypeSummaryStatisticsResults.DatasetStatistics attribute) (cellarium.cas.models.CellTypeSummaryStatisticsResults.SummaryStatistics attribute) module cellarium.cas.client

N

neighbors (cellarium.cas.models.MatrixQueryResults.MatrixQueryResult attribute)

O

ORGANISM (cellarium.cas.constants.CellMetadataFeatures attribute) organism (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute)

ORGANISM_ONTOLOGY_TERM_ID (cellarium.cas.constants.CellMetadataFeatures attribute) organism_ontology_term_id (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) OVER_THRESHOLD (cellarium.cas.postprocessing.ontology_aware.CellOntologyScoresAggregationDomain attribute)

P

p25_distance (cellarium.cas.models.CellTypeSummaryStatisticsResults.SummaryStatistics attribute)

p75_distance (cellarium.cas.models.CellTypeSummaryStatisticsResults.SummaryStatistics attribute) print_user_quota() (cellarium.cas.client.CASClient method)

Q

query_cell_id (cellarium.cas.models.CellTypeOntologyAwareResults.OntologyAwareAnnotation attribute) (cellarium.cas.models.CellTypeSummaryStatisticsResults.NeighborhoodAnnotation attribute) (cellarium.cas.models.MatrixQueryResults.MatrixQueryResult attribute)

query_cells_by_ids() (cellarium.cas.client.CASClient method)

R

RAW_X (cellarium.cas.constants.CountMatrixInput attribute)

run() (cellarium.cas.visualization.CASCircularTreePlotUMAPDashApp method)

S

score (cellarium.cas.models.CellTypeOntologyAwareResults.Match attribute) search_10x_h5_file() (cellarium.cas.client.CASClient method) search_anndata() (cellarium.cas.client.CASClient method) search_matrix() (cellarium.cas.client.CASClient method) SELF_REPORTED_ETHNICITY (cellarium.cas.constants.CellMetadataFeatures attribute) self_reported_ethnicity (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) SELF_REPORTED_ETHNICITY_ONTOLOGY_TERM_ID (cellarium.cas.constants.CellMetadataFeatures attribute)

self_reported_ethnicity_ontology_term_id (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) SEX (cellarium.cas.constants.CellMetadataFeatures attribute) sex (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) SEX_ONTOLOGY_TERM_ID (cellarium.cas.constants.CellMetadataFeatures attribute) sex_ontology_term_id (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) SUSPENSION_TYPE (cellarium.cas.constants.CellMetadataFeatures attribute) suspension_type (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute)

T

TISSUE (cellarium.cas.constants.CellMetadataFeatures attribute) tissue (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) TISSUE_ONTOLOGY_TERM_ID (cellarium.cas.constants.CellMetadataFeatures attribute) tissue_ontology_term_id (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute)

TOTAL_MRNA_UMIS (cellarium.cas.constants.CellMetadataFeatures attribute) total_mrna_umis (cellarium.cas.models.CellQueryResults.CellariumCellMetadata attribute) total_neighbors (cellarium.cas.models.CellTypeOntologyAwareResults.OntologyAwareAnnotation attribute) total_neighbors_unrecognized (cellarium.cas.models.CellTypeOntologyAwareResults.OntologyAwareAnnotation attribute) total_weight (cellarium.cas.models.CellTypeOntologyAwareResults.OntologyAwareAnnotation attribute)

V

validate_and_sanitize_input_data() (cellarium.cas.client.CASClient method)

validate_model_name() (cellarium.cas.client.CASClient method) validate_version() (cellarium.cas.client.CASClient method)

X

X (cellarium.cas.constants.CountMatrixInput attribute)