Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W | Z A abandon_label_claim() (cytearc.datastore.pipeline_accessor.PipelineAccessor method) active_index() (cytearc.metadata.MetaData method) activeIdentity (cytearc.SeuratImportResult attribute) add_grouped_assay() (cytearc.datastore.datastore.DataStore method) add_melded_assay() (cytearc.datastore.datastore.DataStore method) ADTassay (class in cytearc.assay) aggregation() (cytearc.datastore.namespaces.TrajectoryAccessor method) analysisAssay (cytearc.H5adImportResult attribute) ann_index() (cytearc.datastore.namespaces.GraphAccessor method) applies (cytearc.storage.operation_revisions.OperationRevision attribute) artifact (cytearc.EnrichmentResult attribute) ARTIFACT_KINDS (in module cytearc.storage) ArtifactAccessor (class in cytearc.datastore.artifact_accessor) ArtifactLineage (class in cytearc) ArtifactRef (class in cytearc) ArtifactResolutionError (class in cytearc) ArtifactStatus (class in cytearc) Assay (class in cytearc.assay) assay (cytearc.EnrichmentResult attribute) (cytearc.metadata.membership.UnmeasuredCellsError attribute) assay_feature_slices() (cytearc.readers.H5adReader method) assay_membership() (cytearc.readers.H5adReader method) assay_names (cytearc.datastore.datastore.DataStore property) assayFeats (cytearc.readers.CrH5Reader attribute) (cytearc.readers.CrReader attribute) AssayMergePlan (class in cytearc.merge) assayName (cytearc.writers.H5adToZarr attribute) (cytearc.writers.SparseToZarr attribute) assayNames (cytearc.H5adImportResult attribute) (cytearc.SeuratImportResult attribute) assayType (cytearc.assay.Assay property) ATACassay (class in cytearc.assay) attrs (cytearc.assay.Assay attribute) aucell() (cytearc.datastore.namespaces.ScoresAccessor method) auto_filter() (cytearc.datastore.namespaces.QcAccessor method) autoNames (cytearc.readers.CrH5Reader attribute) (cytearc.readers.CrReader attribute) B bucket (cytearc.cytebase.Release property) build_reference() (cytearc.datastore.namespaces.MappingAccessor method) C Catalog (class in cytearc.cytebase) CatalogResults (class in cytearc.cytebase.display) categorical (cytearc.metadata.CellValues attribute) CategoricalScale (class in cytearc.plotting) catNamesKey (cytearc.readers.H5adReader attribute) cell_count (cytearc.cytebase.DatasetEntry property) cell_cycle() (cytearc.datastore.namespaces.ScoresAccessor method) cell_ids (cytearc.metadata.CellValues attribute) cell_ids() (cytearc.readers.CSVReader method) (cytearc.readers.H5adReader method) cell_idx (cytearc.metadata.CellValues attribute) cell_index (cytearc.EnrichmentResult attribute) cell_key (cytearc.metadata.membership.UnmeasuredCellsError attribute) cell_names() (cytearc.readers.CrDirReader method) (cytearc.readers.CrH5Reader method) (cytearc.readers.CrReader method) cell_selection (cytearc.EnrichmentResult attribute) (cytearc.MappingResult property) (cytearc.metadata.CellValues attribute) CELL_VALUE_NAMES (in module cytearc.metadata.selection) cellAttrsKey (cytearc.readers.H5adReader attribute) cellDataDtypes (cytearc.readers.CSVReader attribute) CellField (class in cytearc.plotting) cellIdsKey (cytearc.readers.H5adReader attribute) cells (cytearc.assay.Assay attribute) cellSelection (cytearc.H5adImportResult attribute) (cytearc.SeuratImportResult attribute) CellValues (class in cytearc.metadata) change (cytearc.storage.operation_revisions.OperationRevision attribute) check_destination() (in module cytearc.storage.destinations) chunkBytes (cytearc.storage.count_matrix.CountMatrixPolicy attribute) chunked_to_zarr() (in module cytearc.writers) chunksPerShard (cytearc.storage.count_matrix.CountMatrixPolicy property) citation (cytearc.cytebase.DatasetEntry property) clean_array() (in module cytearc) clisi_knn() (in module cytearc.metrics) close() (cytearc.readers.CrH5Reader method) cluster_connectivity() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) cluster_keys (cytearc.readers.H5adReader attribute) cluster_tree() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) clusterArtifacts (cytearc.H5adImportResult attribute) ClustersAccessor (class in cytearc.datastore.namespaces) ClusterSeparabilityResult (class in cytearc.metrics) ColorScale (class in cytearc.plotting) column (cytearc.metadata.membership.UnmeasuredCellsError attribute) columns (cytearc.metadata.MetaData property) CompareAccessor (class in cytearc.datastore.namespaces) ComponentResult (class in cytearc.merge) compose_results() (in module cytearc.plotting) composition() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) compute_batch_mixing() (cytearc.datastore.namespaces.IntegrationAccessor method) compute_bulk() (cytearc.datastore.namespaces.CompareAccessor method) compute_clisi() (cytearc.datastore.namespaces.IntegrationAccessor method) compute_cluster_separability() (cytearc.datastore.namespaces.IntegrationAccessor method) compute_concordance() (cytearc.datastore.namespaces.ClustersAccessor method) compute_graph_connectivity() (cytearc.datastore.namespaces.IntegrationAccessor method) compute_graph_silhouette() (cytearc.datastore.namespaces.IntegrationAccessor method) compute_ilisi() (cytearc.datastore.namespaces.IntegrationAccessor method) compute_imputed() (cytearc.datastore.namespaces.ImputationAccessor method) compute_lisi() (in module cytearc.metrics) compute_scores() (cytearc.datastore.namespaces.MappingAccessor method) compute_with_progress() (in module cytearc) computeWorkers (cytearc.storage.io_policy.StorageIoPolicy attribute) configure_output() (in module cytearc) connect() (in module cytearc.cytebase) connect_catalog() (cytearc.cytebase.Catalog method) connectivity() (cytearc.datastore.namespaces.GraphAccessor method) consume() (cytearc.readers.CrDirReader method) (cytearc.readers.CrH5Reader method) (cytearc.readers.CrReader method) (cytearc.readers.CSVReader method) (cytearc.readers.H5adReader method) (cytearc.readers.MtxReader method) consume_dataset() (cytearc.readers.H5adReader method) consume_group() (cytearc.readers.H5adReader method) consume_row_range() (cytearc.readers.H5adReader method) consumeDtype (cytearc.readers.H5adReader property) controlled_compute() (in module cytearc) count_storage_dtype() (in module cytearc.storage.count_dtype) count_value_ranges() (cytearc.readers.CrDirReader method) (cytearc.readers.CrH5Reader method) (cytearc.readers.CrReader method) (cytearc.readers.H5adReader method) (cytearc.readers.MtxReader method) countDtype (cytearc.readers.CSVReader attribute) CountMatrixPolicy (class in cytearc.storage.count_matrix) countRange (cytearc.readers.CSVReader attribute) CountValueRange (class in cytearc.utils.count_values) cr (cytearc.writers.CrToZarr attribute) CrDirReader (class in cytearc.readers) create_destination() (in module cytearc.storage.destinations) create_zarr_count_assay() (in module cytearc.writers) create_zarr_dataset() (in module cytearc.writers) create_zarr_obj_array() (in module cytearc.writers) CrH5Reader (class in cytearc.readers) CrReader (class in cytearc.readers) CrToZarr (class in cytearc.writers) csvr (cytearc.writers.CSVtoZarr attribute) CSVReader (class in cytearc.readers) CSVtoZarr (class in cytearc.writers) current_model_digest() (cytearc.MappingReference method) current_revision (cytearc.ArtifactStatus property) custom() (cytearc.datastore.namespaces.ReductionAccessor method) cytearc.logger (built-in variable) cytearc.metrics module cytearc.plotting module cytearc.tqdm_params (built-in variable) D data (cytearc.EnrichmentResult attribute) dataset() (cytearc.cytebase.Catalog method) DatasetEntry (class in cytearc.cytebase) DataStore (class in cytearc.datastore.datastore) DataStoreMerge (class in cytearc.merge) DataStorePlotAccessor (class in cytearc.datastore.plot_accessor) DataStoreSummary (class in cytearc) default_block_rows() (cytearc.metadata.MetaData method) defaultAssay (cytearc.SeuratImportResult attribute) DensityOverlay (class in cytearc.plotting) describe() (cytearc.cytebase.DatasetEntry method) detected() (cytearc.datastore.namespaces.FeaturesAccessor method) diffusion() (cytearc.datastore.namespaces.ImputationAccessor method) discard_interrupted_assay() (cytearc.datastore.datastore.DataStore method) distribution() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) dotplot() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) doublets() (cytearc.datastore.namespaces.QcAccessor method) download() (cytearc.cytebase.Repository method) download_dataset() (cytearc.cytebase.Repository method) drop() (cytearc.metadata.MetaData method) dump() (cytearc.merge.DataStoreMerge method) (cytearc.SeuratToZarr method) (cytearc.writers.CrToZarr method) (cytearc.writers.CSVtoZarr method) (cytearc.writers.H5adToZarr method) (cytearc.writers.SparseToZarr method) (cytearc.writers.SubsetZarr method) E elbow() (in module cytearc.plotting) embedding() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.cytebase) (in module cytearc.plotting) embedding_coordinates() (in module cytearc.cytebase) embedding_raster() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) embedding_roles (cytearc.readers.H5adReader attribute) embeddingArtifacts (cytearc.H5adImportResult attribute) embeddings() (in module cytearc.cytebase) EmbeddingsAccessor (class in cytearc.datastore.namespaces) EnrichmentResult (class in cytearc) export_csv() (cytearc.datastore.namespaces.MarkersAccessor method) ExternalArtifactRef (class in cytearc.storage.refs) F fate() (cytearc.datastore.namespaces.TrajectoryAccessor method) FateMappingResult (class in cytearc) feat_ids() (cytearc.readers.H5adReader method) feat_names() (cytearc.readers.H5adReader method) featIdsKey (cytearc.readers.H5adReader attribute) featNamesKey (cytearc.readers.H5adReader attribute) feats (cytearc.assay.Assay attribute) feature_ids (cytearc.PseudotimeAggregationResult property) feature_ids() (cytearc.readers.CrDirReader method) (cytearc.readers.CrReader method) (cytearc.readers.CSVReader method) feature_names (cytearc.PseudotimeAggregationResult property) feature_names() (cytearc.readers.CrDirReader method) (cytearc.readers.CrReader method) feature_percentage() (cytearc.datastore.namespaces.QcAccessor method) feature_selection (cytearc.EnrichmentResult attribute) (cytearc.MappingResult property) feature_types() (cytearc.readers.CrDirReader method) (cytearc.readers.CrReader method) (cytearc.readers.H5adReader method) featureAttrsKey (cytearc.readers.H5adReader attribute) FeatureRef (class in cytearc.plotting) FeaturesAccessor (class in cytearc.datastore.namespaces) fetch() (cytearc.metadata.MetaData method) fetch_all() (cytearc.metadata.MetaData method) fetch_all_columns() (cytearc.metadata.MetaData method) fetch_cell_column() (cytearc.MappingReference method) filter() (cytearc.datastore.namespaces.QcAccessor method) find() (cytearc.datastore.artifact_accessor.ArtifactAccessor method) find_datasets() (cytearc.cytebase.Catalog method) fingerprint_assay (cytearc.storage.refs.ExternalArtifactRef property) fit_harmony() (in module cytearc.embeddings) G get_assay() (cytearc.datastore.datastore.DataStore method) get_cell_columns() (cytearc.readers.CrDirReader method) (cytearc.readers.CrReader method) (cytearc.readers.H5adReader method) (cytearc.readers.MtxReader method) get_cell_vals() (cytearc.datastore.datastore.DataStore method) get_dtype() (cytearc.metadata.MetaData method) get_feat_columns() (cytearc.readers.H5adReader method) get_feature_columns() (cytearc.readers.CrDirReader method) (cytearc.readers.CrH5Reader method) (cytearc.readers.CrReader method) (cytearc.readers.MtxReader method) get_index_by() (cytearc.metadata.MetaData method) graph_connectivity() (in module cytearc.metrics) graph_qc() (in module cytearc.plotting) GraphAccessor (class in cytearc.datastore.namespaces) grep() (cytearc.metadata.MetaData method) groupCodes (cytearc.readers.H5adReader attribute) grp (cytearc.readers.CrH5Reader attribute) grpNames (cytearc.readers.CrH5Reader attribute) (cytearc.readers.CrReader attribute) H h5 (cytearc.readers.H5adReader attribute) h5ad (cytearc.writers.H5adToZarr attribute) H5adImportResult (class in cytearc) H5adInspectResult (class in cytearc) H5adReader (class in cytearc.readers) H5adToZarr (class in cytearc.writers) h5obj (cytearc.readers.CrH5Reader attribute) harmony() (cytearc.datastore.namespaces.ReductionAccessor method) HarmonyResult (class in cytearc.embeddings) head() (cytearc.metadata.MetaData method) Highlight (class in cytearc.plotting) highly_variable_features() (in module cytearc.plotting) hto_demultiplexing() (cytearc.datastore.namespaces.QcAccessor method) hvgs() (cytearc.datastore.namespaces.FeaturesAccessor method) I id (cytearc.cytebase.DatasetEntry property) ilisi_knn() (in module cytearc.metrics) ImputationAccessor (class in cytearc.datastore.namespaces) index_to_bool() (cytearc.metadata.MetaData method) initialization() (cytearc.datastore.namespaces.EmbeddingsAccessor method) input_ref() (cytearc.ArtifactStatus method) insert() (cytearc.metadata.MetaData method) inspect() (cytearc.datastore.artifact_accessor.ArtifactAccessor method) inspect_artifact() (in module cytearc.storage) inspect_h5ad() (in module cytearc) inspect_mtx() (in module cytearc) inspect_seurat() (in module cytearc) integral (cytearc.utils.count_values.CountValueRange attribute) IntegrationAccessor (class in cytearc.datastore.namespaces) is_current (cytearc.ArtifactStatus property) iter_normed_feature_wise() (cytearc.assay.Assay method) (cytearc.assay.RNAassay method) iter_row_blocks() (cytearc.metadata.MetaData method) L label_concordance_score() (in module cytearc.metrics) label_panels() (in module cytearc.plotting) label_vote_shares() (cytearc.LabelTransferResult method) labels (cytearc.LabelTransferResult property) LabelTransferResult (class in cytearc) latest (cytearc.cytebase.Release property) LegendSpec (class in cytearc.plotting) leiden() (cytearc.datastore.namespaces.ClustersAccessor method) lineage() (cytearc.datastore.artifact_accessor.ArtifactAccessor method) lisi_batch_mixing_score() (in module cytearc.metrics) list() (cytearc.datastore.artifact_accessor.ArtifactAccessor method) list_artifacts() (in module cytearc.storage) list_datasets() (cytearc.cytebase.Repository method) list_repositories() (in module cytearc.cytebase) list_runs() (cytearc.datastore.pipeline_accessor.PipelineAccessor method) list_terms() (cytearc.cytebase.Catalog method) load() (cytearc.datastore.artifact_accessor.ArtifactAccessor method) (cytearc.datastore.namespaces.GraphAccessor method) (cytearc.datastore.namespaces.MarkersAccessor method) (cytearc.datastore.namespaces.ScoresAccessor method) load_aggregation() (cytearc.datastore.namespaces.TrajectoryAccessor method) load_diffusion() (cytearc.datastore.namespaces.ImputationAccessor method) load_fate() (cytearc.datastore.namespaces.TrajectoryAccessor method) load_label_transfer() (cytearc.datastore.namespaces.MappingAccessor method) load_markers() (cytearc.datastore.namespaces.TrajectoryAccessor method) load_paris() (cytearc.datastore.namespaces.ClustersAccessor method) load_pseudotime() (cytearc.datastore.namespaces.TrajectoryAccessor method) load_reference() (cytearc.datastore.namespaces.MappingAccessor method) load_result() (cytearc.datastore.namespaces.MappingAccessor method) load_tests() (cytearc.datastore.namespaces.CompareAccessor method) load_values() (cytearc.datastore.artifact_accessor.ArtifactAccessor method) load_zarr() (in module cytearc) lsi() (cytearc.datastore.namespaces.ReductionAccessor method) M mapping_calibration() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) mapping_confusion() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) mapping_evidence() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) mapping_score() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) MappingAccessor (class in cytearc.datastore.namespaces) MappingReference (class in cytearc) MappingResult (class in cytearc) marker_heatmap() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) markers() (cytearc.datastore.namespaces.TrajectoryAccessor method) MarkersAccessor (class in cytearc.datastore.namespaces) mat (cytearc.writers.SparseToZarr attribute) materialize_csc() (cytearc.readers.H5adReader method) materialized_csr_bytes() (cytearc.readers.H5adReader method) matrix_dtype (cytearc.readers.CrDirReader property) (cytearc.readers.CrH5Reader property) (cytearc.readers.CrReader property) (cytearc.readers.MtxReader property) matrixKey (cytearc.readers.H5adReader attribute) matrixplot() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) max_batch_nnz() (cytearc.readers.H5adReader method) max_window_nnz() (cytearc.readers.CrDirReader method) (cytearc.readers.CrH5Reader method) (cytearc.readers.CrReader method) (cytearc.readers.MtxReader method) maximum (cytearc.utils.count_values.CountValueRange attribute) membership_strength() (cytearc.datastore.namespaces.ClustersAccessor method) MergePlan (class in cytearc.merge) MergeResult (class in cytearc.merge) MetaData (class in cytearc.metadata) method (cytearc.EnrichmentResult attribute) missing (cytearc.metadata.CellValues attribute) modalities() (cytearc.datastore.namespaces.IntegrationAccessor method) modality_weights() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) module cytearc.metrics cytearc.plotting mount_datastore() (cytearc.cytebase.Catalog method) (in module cytearc) MtxCandidate (class in cytearc.readers) MtxReader (class in cytearc.readers) MtxToZarr (in module cytearc.writers) multi_sift() (cytearc.metadata.MetaData method) N n_cells (cytearc.LabelTransferResult property) name (cytearc.assay.Assay attribute) nCells (cytearc.readers.CrH5Reader attribute) (cytearc.readers.CrReader attribute) (cytearc.readers.CSVReader attribute) (cytearc.readers.H5adReader attribute) neighbors() (cytearc.datastore.namespaces.GraphAccessor method) nFeatures (cytearc.readers.CrH5Reader attribute) (cytearc.readers.CrReader attribute) (cytearc.readers.CSVReader attribute) (cytearc.readers.H5adReader attribute) norm_dummy() (in module cytearc.assay) NormalizationSpec (class in cytearc.plotting) normalize() (cytearc.datastore.namespaces.FeaturesAccessor method) normed() (cytearc.assay.Assay method) (cytearc.assay.ATACassay method) (cytearc.assay.RNAassay method) normMethod (cytearc.assay.ADTassay attribute) (cytearc.assay.Assay attribute) (cytearc.assay.RNAassay attribute) notices (cytearc.SeuratImportResult attribute) nthreads (cytearc.assay.Assay attribute) O open() (cytearc.datastore.pipeline_accessor.PipelineAccessor method) open_datastore() (cytearc.cytebase.Catalog method) operation (cytearc.metadata.membership.UnmeasuredCellsError attribute) OperationRevision (class in cytearc.storage.operation_revisions) P paris() (cytearc.datastore.namespaces.ClustersAccessor method) ParisClusterDiagnostic (class in cytearc.clustering) ParisClusteringResult (class in cytearc.clustering) pca() (cytearc.datastore.namespaces.ReductionAccessor method) permute_into_chunks() (in module cytearc) pipeline (cytearc.datastore.datastore.DataStore property) PipelineAccessor (class in cytearc.datastore.pipeline_accessor) PipelineEvent (class in cytearc.datastore.pipeline_accessor) PipelineExecutionError (class in cytearc) PipelineRun (class in cytearc) plan() (cytearc.merge.DataStoreMerge method) PlotOutput (class in cytearc.plotting) PlotOutputSettings (class in cytearc.plotting) PlotPanelTarget (class in cytearc.plotting) PlotProvenance (class in cytearc.plotting) PlotRecipe (class in cytearc.plotting) PlotRecipeResult (class in cytearc.plotting) PlotResult (class in cytearc.plotting) plots (cytearc.datastore.datastore.DataStore property) PlotStep (class in cytearc.plotting) policy (cytearc.writers.H5adToZarr attribute) prediction_sets() (cytearc.LabelTransferResult method) prevalent_peaks() (cytearc.datastore.namespaces.FeaturesAccessor method) producer_batch_staging_bytes() (cytearc.readers.H5adReader method) producer_staging_bytes() (cytearc.readers.CrDirReader method) (cytearc.readers.CrH5Reader method) (cytearc.readers.CrReader method) (cytearc.readers.MtxReader method) pseudotime() (cytearc.datastore.namespaces.TrajectoryAccessor method) pseudotime_heatmap() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) PseudotimeAggregationResult (class in cytearc) PseudotimeMarkerResult (class in cytearc) PseudotimeScoreResult (class in cytearc) Q qc() (in module cytearc.plotting) QcAccessor (class in cytearc.datastore.namespaces) query() (cytearc.cytebase.Catalog method) R rawData (cytearc.assay.Assay attribute) read_gmt() (in module cytearc) readWorkers (cytearc.storage.io_policy.StorageIoPolicy attribute) reclassify_features() (cytearc.readers.CrDirReader method) (cytearc.readers.CrReader method) record() (cytearc.cytebase.DatasetEntry method) ReductionAccessor (class in cytearc.datastore.namespaces) reductionArtifacts (cytearc.SeuratImportResult attribute) refuse_pending_assays() (in module cytearc.storage.destinations) relabel_by_overlap() (cytearc.datastore.namespaces.ClustersAccessor method) Release (class in cytearc.cytebase) release (cytearc.storage.operation_revisions.OperationRevision attribute) releases() (in module cytearc.cytebase) remedy (cytearc.metadata.membership.UnmeasuredCellsError attribute) rename_assays() (cytearc.readers.CrDirReader method) (cytearc.readers.CrReader method) report() (cytearc.PipelineRun method) Repository (class in cytearc.cytebase) rescale_array() (in module cytearc) reset_key() (cytearc.metadata.MetaData method) resolve() (cytearc.datastore.namespaces.FeaturesAccessor method) revision (cytearc.ArtifactStatus property) (cytearc.storage.operation_revisions.OperationRevision attribute) RNAassay (class in cytearc.assay) rolling_window() (in module cytearc) run() (cytearc.datastore.namespaces.MappingAccessor method) (cytearc.datastore.pipeline_accessor.PipelineAccessor method) run_recipe() (cytearc.datastore.plot_accessor.DataStorePlotAccessor method) (in module cytearc.plotting) S save() (cytearc.plotting.PlotResult method) save_provenance() (cytearc.plotting.PlotResult method) scalar (cytearc.assay.RNAassay attribute) score_features() (cytearc.assay.Assay method) ScoresAccessor (class in cytearc.datastore.namespaces) search() (cytearc.cytebase.Catalog method) (cytearc.datastore.namespaces.MarkersAccessor method) select_cells() (cytearc.datastore.datastore.DataStore method) select_measured_cells() (cytearc.datastore.datastore.DataStore method) selected (cytearc.metadata.membership.UnmeasuredCellsError attribute) set_verbosity() (in module cytearc) SeuratImportResult (class in cytearc) SeuratInspectResult (class in cytearc) SeuratReader (class in cytearc) SeuratToZarr (class in cytearc) sf (cytearc.assay.Assay attribute) (cytearc.assay.RNAassay attribute) show_zarr_tree() (cytearc.datastore.datastore.DataStore method) sift() (cytearc.metadata.MetaData method) silhouette_scoring() (in module cytearc.metrics) SizeScale (class in cytearc.plotting) snapshot() (cytearc.datastore.namespaces.FeaturesAccessor method) snapshot_cell_selection() (cytearc.DataStore method) snapshot_cluster_labels() (cytearc.datastore.datastore.DataStore method) source (cytearc.metadata.CellValues attribute) source_embeddings() (cytearc.cytebase.DatasetEntry method) source_names (cytearc.EnrichmentResult attribute) source_sizes (cytearc.EnrichmentResult attribute) sourceMatrixDtype (cytearc.readers.H5adReader attribute) SparseToZarr (class in cytearc.writers) StatisticalTestResult (class in cytearc.features.statistical) storage_path (cytearc.EnrichmentResult attribute) storageDtypes (cytearc.writers.H5adToZarr attribute) StorageIoPolicy (class in cytearc.storage.io_policy) StudyDesign (class in cytearc.plotting) subset_assay_zarr() (in module cytearc.writers) SubsetZarr (class in cytearc.writers) summary() (cytearc.DataStore method) superseded_by (cytearc.ArtifactStatus property) T test() (cytearc.datastore.namespaces.CompareAccessor method) theme_context() (in module cytearc.plotting) THEMES (in module cytearc.plotting) title (cytearc.cytebase.DatasetEntry property) to_anndata() (cytearc.datastore.datastore.DataStore method) to_dict() (cytearc.DataStoreSummary method) to_h5ad() (in module cytearc.writers) to_markdown() (cytearc.cytebase.display.CatalogResults method) to_mtx() (in module cytearc.writers) to_pandas() (cytearc.metadata.CellValues method) to_pandas_dataframe() (cytearc.metadata.MetaData method) tqdmbar() (in module cytearc) TrajectoryAccessor (class in cytearc.datastore.namespaces) transfer_labels() (cytearc.datastore.namespaces.MappingAccessor method) tsne() (cytearc.datastore.namespaces.EmbeddingsAccessor method) U umap() (cytearc.datastore.namespaces.EmbeddingsAccessor method) unitBytes (cytearc.storage.count_matrix.CountMatrixPolicy attribute) universe() (cytearc.datastore.namespaces.FeaturesAccessor method) unmeasured (cytearc.metadata.membership.UnmeasuredCellsError attribute) UnmeasuredCellsError update() (cytearc.utils.count_values.CountValueRange method) update_key() (cytearc.metadata.MetaData method) V validate_dataset_fingerprint() (cytearc.MappingReference method) validate_frozen_axes() (cytearc.MappingReference method) value (cytearc.metadata.CellValues attribute) values (cytearc.metadata.CellValues attribute) W waggr() (cytearc.datastore.namespaces.ScoresAccessor method) write_renorm_subset_to_zarr() (in module cytearc.writers) writeWorkers (cytearc.storage.io_policy.StorageIoPolicy attribute) Z z (cytearc.assay.Assay attribute) (cytearc.writers.CrToZarr attribute) (cytearc.writers.CSVtoZarr attribute) (cytearc.writers.H5adToZarr attribute) (cytearc.writers.SparseToZarr attribute) zw (cytearc.datastore.datastore.DataStore property)
