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() (scarf.datastore.pipeline_accessor.PipelineAccessor method) active_index() (scarf.metadata.MetaData method) activeIdentity (scarf.SeuratImportResult attribute) add_grouped_assay() (scarf.datastore.datastore.DataStore method) add_melded_assay() (scarf.datastore.datastore.DataStore method) ADTassay (class in scarf.assay) all features analysisAssay (scarf.H5adImportResult attribute) AnalysisError analyze_rna() (in module scarf.agent) artifact (scarf.EnrichmentResult attribute) artifact lineage ARTIFACT_KINDS (in module scarf.storage) ArtifactLineage (class in scarf) ArtifactRef (class in scarf) ArtifactResolutionError (class in scarf) ArtifactStatus (class in scarf) assay Assay (class in scarf.assay) assay (scarf.EnrichmentResult attribute) assay_feature_slices() (scarf.readers.H5adReader method) assay_names (scarf.datastore.datastore.DataStore property) assayFeats (scarf.readers.CrH5Reader attribute) (scarf.readers.CrReader attribute) AssayMergePlan (class in scarf.merge) assayName (scarf.writers.H5adToZarr attribute) (scarf.writers.LoomToZarr attribute) (scarf.writers.SparseToZarr attribute) assayNames (scarf.H5adImportResult attribute) (scarf.SeuratImportResult attribute) ATACassay (class in scarf.assay) attrs (scarf.assay.Assay attribute) auto_filter_cells() (scarf.datastore.datastore.DataStore method) AutomatedWorkflowResult (class in scarf.agent) autoNames (scarf.readers.CrH5Reader attribute) (scarf.readers.CrReader attribute) B batch correction build_ann_index() (scarf.DataStore method) build_connectivity_map() (scarf.DataStore method) build_embedding_initialization() (scarf.DataStore method) build_mapping_reference() (scarf.DataStore method) C calc_membership_strength() (scarf.datastore.datastore.DataStore method) calibrate_label_transfer_threshold() (scarf.DataStore static method) CategoricalScale (class in scarf.plotting) catNamesKey (scarf.readers.H5adReader attribute) cell key cell_ids() (scarf.readers.CSVReader method) (scarf.readers.H5adReader method) (scarf.readers.LoomReader method) cell_index (scarf.EnrichmentResult attribute) cell_names() (scarf.readers.CrDirReader method) (scarf.readers.CrH5Reader method) (scarf.readers.CrReader method) (scarf.readers.LoomReader method) cell_selection (scarf.EnrichmentResult attribute) (scarf.MappingResult property) cellAttrsKey (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) CellField (class in scarf.plotting) cellIdsKey (scarf.readers.H5adReader attribute) cellNamesKey (scarf.readers.LoomReader attribute) cells (scarf.assay.Assay attribute) cellSelection (scarf.H5adImportResult attribute) (scarf.SeuratImportResult attribute) chunkBytes (scarf.storage.count_matrix.CountMatrixPolicy attribute) chunked_to_zarr() (in module scarf.writers) chunksPerShard (scarf.storage.count_matrix.CountMatrixPolicy property) clean_array() (in module scarf) cLISI clisi_knn() (in module scarf.metrics) close() (scarf.readers.CrH5Reader method) cluster_connectivity() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) cluster_keys (scarf.readers.H5adReader attribute) cluster_tree() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) clusterArtifacts (scarf.H5adImportResult attribute) ClusterSeparabilityResult (class in scarf.metrics) collect_legends() (in module scarf.plotting) ColorScale (class in scarf.plotting) columns (scarf.metadata.MetaData property) ComponentResult (class in scarf.merge) compose_results() (in module scarf.plotting) composition() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) compute_lisi() (in module scarf.metrics) compute_with_progress() (in module scarf) computeWorkers (scarf.storage.io_policy.StorageIoPolicy attribute) configure_output() (in module scarf) connect() (in module scarf.cytebase) consume() (scarf.readers.CrDirReader method) (scarf.readers.CrH5Reader method) (scarf.readers.CrReader method) (scarf.readers.CSVReader method) (scarf.readers.H5adReader method) (scarf.readers.LoomReader method) (scarf.readers.MtxReader method) consume_dataset() (scarf.readers.H5adReader method) consume_group() (scarf.readers.H5adReader method) consume_row_range() (scarf.readers.H5adReader method) controlled_compute() (in module scarf) coordinate_melding() (in module scarf) count matrix CountMatrixPolicy (class in scarf.storage.count_matrix) cr (scarf.writers.CrToZarr attribute) CrDirReader (class in scarf.readers) create_zarr_count_assay() (in module scarf.writers) create_zarr_dataset() (in module scarf.writers) create_zarr_obj_array() (in module scarf.writers) CrH5Reader (class in scarf.readers) CrReader (class in scarf.readers) CrToZarr (class in scarf.writers) csvr (scarf.writers.CSVtoZarr attribute) CSVReader (class in scarf.readers) CSVtoZarr (class in scarf.writers) current_model_digest() (scarf.MappingReference method) D d_apply() (scarf.GffReader static method) data (scarf.EnrichmentResult attribute) DataStore (class in scarf.datastore.datastore) DataStoreMerge (class in scarf.merge) DataStorePlotAccessor (class in scarf.datastore.plot_accessor) DataStoreSummary (class in scarf) default_block_rows() (scarf.metadata.MetaData method) defaultAssay (scarf.SeuratImportResult attribute) DensityOverlay (class in scarf.plotting) densMAP distribution() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) dotplot() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) download() (scarf.cytebase.Repository method) download_dataset() (scarf.cytebase.Repository method) drop() (scarf.metadata.MetaData method) dump() (scarf.merge.DataStoreMerge method) (scarf.SeuratToZarr method) (scarf.writers.CrToZarr method) (scarf.writers.CSVtoZarr method) (scarf.writers.H5adToZarr method) (scarf.writers.LoomToZarr method) (scarf.writers.SparseToZarr method) (scarf.writers.SubsetZarr method) E elbow() (in module scarf.plotting) embedding() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) embedding_raster() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) embedding_roles (scarf.readers.H5adReader attribute) embeddingArtifacts (scarf.H5adImportResult attribute) EnrichmentResult (class in scarf) export_markers_to_csv() (scarf.datastore.datastore.DataStore method) ExternalArtifactRef (class in scarf.storage.refs) F FateMappingResult (class in scarf) feat_ids() (scarf.readers.H5adReader method) feat_names() (scarf.readers.H5adReader method) featIdsKey (scarf.readers.H5adReader attribute) featNamesKey (scarf.readers.H5adReader attribute) feats (scarf.assay.Assay attribute) feature selection feature_ids (scarf.PseudotimeAggregationResult property) feature_ids() (scarf.readers.CrDirReader method) (scarf.readers.CrReader method) (scarf.readers.CSVReader method) (scarf.readers.LoomReader method) feature_names (scarf.PseudotimeAggregationResult property) feature_names() (scarf.readers.CrDirReader method) (scarf.readers.CrReader method) (scarf.readers.LoomReader method) feature_selection (scarf.EnrichmentResult attribute) (scarf.MappingResult property) feature_types() (scarf.readers.CrDirReader method) (scarf.readers.CrReader method) (scarf.readers.H5adReader method) featureAttrsKey (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) featureIdsKey (scarf.readers.LoomReader attribute) featureNamesKey (scarf.readers.LoomReader attribute) FeatureRef (class in scarf.plotting) FeatureSummary (class in scarf.plotting) fetch() (scarf.metadata.MetaData method) fetch_all() (scarf.metadata.MetaData method) fetch_all_columns() (scarf.metadata.MetaData method) fetch_cell_column() (scarf.MappingReference method) fetch_header_lines() (scarf.GffReader method) fetch_layout() (scarf.MappingReference method) filter_cells() (scarf.datastore.datastore.DataStore method) fit_harmony() (in module scarf.embeddings) fn (scarf.writers.CSVtoZarr attribute) (scarf.writers.LoomToZarr attribute) (scarf.writers.SparseToZarr attribute) G get_assay() (scarf.datastore.datastore.DataStore method) get_body() (scarf.GffReader method) get_cell_attrs() (scarf.readers.LoomReader method) get_cell_columns() (scarf.readers.CrDirReader method) (scarf.readers.CrReader method) (scarf.readers.H5adReader method) (scarf.readers.MtxReader method) get_cell_vals() (scarf.datastore.datastore.DataStore method) get_dtype() (scarf.metadata.MetaData method) get_enrichment() (scarf.datastore.datastore.DataStore method) get_feat_columns() (scarf.readers.H5adReader method) get_feature_attrs() (scarf.readers.LoomReader method) get_feature_columns() (scarf.readers.CrDirReader method) (scarf.readers.CrH5Reader method) (scarf.readers.CrReader method) (scarf.readers.MtxReader method) get_ids_names() (scarf.GffReader static method) get_imputed() (scarf.datastore.datastore.DataStore method) get_index_by() (scarf.metadata.MetaData method) get_log_level() (in module scarf) get_mapping_reference() (scarf.DataStore method) get_mapping_result() (scarf.DataStore method) get_mapping_score() (scarf.DataStore method) get_markers() (scarf.agent.AutomatedWorkflowResult method) (scarf.datastore.datastore.DataStore method) get_promoter() (scarf.GffReader method) get_statistical_tests() (scarf.datastore.datastore.DataStore method) get_target_classes() (scarf.DataStore method) get_target_label_evidence() (scarf.DataStore method) GffReader (class in scarf) graph connectivity graph_connectivity() (in module scarf.metrics) graph_qc() (in module scarf.plotting) grep() (scarf.metadata.MetaData method) groupCodes (scarf.readers.H5adReader attribute) grp (scarf.readers.CrH5Reader attribute) grpNames (scarf.readers.CrH5Reader attribute) (scarf.readers.CrReader attribute) H h5 (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) h5ad (scarf.writers.H5adToZarr attribute) H5adImportResult (class in scarf) H5adInspectResult (class in scarf) H5adReader (class in scarf.readers) H5adToZarr (class in scarf.writers) h5obj (scarf.readers.CrH5Reader attribute) Harmony HarmonyResult (class in scarf.embeddings) head() (scarf.metadata.MetaData method) Highlight (class in scarf.plotting) highly variable genes highly_variable_features() (in module scarf.plotting) I iLISI ilisi_knn() (in module scarf.metrics) index_to_bool() (scarf.metadata.MetaData method) infer_storage_dtype() (scarf.readers.H5adReader method) insert() (scarf.metadata.MetaData method) inspect_artifact() (in module scarf.storage) (scarf.DataStore method) inspect_h5ad() (in module scarf) inspect_mtx() (in module scarf) inspect_seurat() (in module scarf) integrate_assays() (scarf.DataStore method) iter_normed_feature_wise() (scarf.assay.Assay method) (scarf.assay.RNAassay method) iter_row_blocks() (scarf.metadata.MetaData method) L label_concordance_score() (in module scarf.metrics) label_panels() (in module scarf.plotting) last_execution_report (scarf.datastore.datastore.DataStore property) LegendSpec (class in scarf.plotting) Leiden clustering lineage() (scarf.DataStore method) LISI lisi_batch_mixing_score() (in module scarf.metrics) list_artifacts() (in module scarf.storage) (scarf.DataStore method) list_datasets() (scarf.cytebase.Repository method) list_files() (scarf.cytebase.Repository method) list_repositories() (in module scarf.cytebase) list_runs() (scarf.datastore.pipeline_accessor.PipelineAccessor method) load_artifact() (scarf.DataStore method) load_diffusion_operator() (scarf.datastore.datastore.DataStore method) load_fate_mapping() (scarf.datastore.datastore.DataStore method) load_graph() (scarf.DataStore method) load_metric_lisi() (scarf.DataStore method) load_paris_clustering() (scarf.datastore.datastore.DataStore method) load_pseudotime_aggregation() (scarf.datastore.datastore.DataStore method) load_pseudotime_markers() (scarf.datastore.datastore.DataStore method) load_pseudotime_scoring() (scarf.datastore.datastore.DataStore method) load_zarr() (in module scarf) loom (scarf.writers.LoomToZarr attribute) LoomReader (class in scarf.readers) LoomToZarr (class in scarf.writers) LSI M make_bulk() (scarf.datastore.datastore.DataStore method) mapping reference mapping_calibration() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) mapping_confusion() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) mapping_evidence() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) mapping_score() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) MappingReference (class in scarf) MappingResult (class in scarf) marker_heatmap() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) mat (scarf.writers.SparseToZarr attribute) materialize_csc() (scarf.readers.H5adReader method) materialized_csr_bytes() (scarf.readers.H5adReader method) matrix_dtype (scarf.readers.CrDirReader property) (scarf.readers.CrH5Reader property) (scarf.readers.CrReader property) (scarf.readers.MtxReader property) matrixDtype (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) matrixKey (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) matrixplot() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) max_batch_nnz() (scarf.readers.H5adReader method) max_window_nnz() (scarf.readers.CrDirReader method) (scarf.readers.CrH5Reader method) (scarf.readers.CrReader method) (scarf.readers.MtxReader method) mean_features() (scarf.assay.Assay method) MergePlan (class in scarf.merge) MergeResult (class in scarf.merge) MetaData (class in scarf.metadata) method (scarf.EnrichmentResult attribute) metric_clisi() (scarf.DataStore method) metric_cluster_separability() (scarf.DataStore method) metric_graph_connectivity() (scarf.DataStore method) metric_graph_silhouette() (scarf.DataStore method) metric_ilisi() (scarf.DataStore method) metric_label_concordance() (scarf.DataStore method) metric_lisi() (scarf.DataStore method) metric_proportional_batch_mixing() (scarf.DataStore method) modality_weights() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) module scarf.metrics scarf.plotting mount_datastore() (in module scarf) MtxCandidate (class in scarf.readers) MtxReader (class in scarf.readers) MtxToZarr (in module scarf.writers) multi_sift() (scarf.metadata.MetaData method) N name (scarf.assay.Assay attribute) nCells (scarf.readers.CrH5Reader attribute) (scarf.readers.CrReader attribute) (scarf.readers.CSVReader attribute) (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) neighbourhood graph nFeatures (scarf.readers.CrH5Reader attribute) (scarf.readers.CrReader attribute) (scarf.readers.CSVReader attribute) (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) norm_dummy() (in module scarf.assay) NormalizationSpec (class in scarf.plotting) normed() (scarf.assay.ADTassay method) (scarf.assay.Assay method) (scarf.assay.ATACassay method) (scarf.assay.RNAassay method) normMethod (scarf.assay.ADTassay attribute) (scarf.assay.Assay attribute) (scarf.assay.RNAassay attribute) notices (scarf.SeuratImportResult attribute) nthreads (scarf.assay.Assay attribute) O open() (scarf.datastore.pipeline_accessor.PipelineAccessor method) open_clone() (scarf.readers.H5adReader method) open_zarr() (scarf.cytebase.Repository method) P Paris clustering ParisClusterDiagnostic (class in scarf.clustering) ParisClusteringResult (class in scarf.clustering) partial PCA permute_into_chunks() (in module scarf) pipeline (scarf.datastore.datastore.DataStore property) PipelineAccessor (class in scarf.datastore.pipeline_accessor) PipelineEvent (class in scarf.datastore.pipeline_accessor) PipelineExecutionError (class in scarf) PipelineRun (class in scarf) plan() (scarf.merge.DataStoreMerge method) plot_embedding() (scarf.agent.AutomatedWorkflowResult method) PlotOutput (class in scarf.plotting) PlotOutputSettings (class in scarf.plotting) PlotPanelTarget (class in scarf.plotting) PlotProvenance (class in scarf.plotting) PlotRecipe (class in scarf.plotting) PlotRecipeResult (class in scarf.plotting) PlotResult (class in scarf.plotting) plots (scarf.datastore.datastore.DataStore property) PlotStep (class in scarf.plotting) producer_batch_staging_bytes() (scarf.readers.H5adReader method) producer_staging_bytes() (scarf.readers.CrDirReader method) (scarf.readers.CrH5Reader method) (scarf.readers.CrReader method) (scarf.readers.MtxReader method) proportion-aware batch mixing provenance pseudotime_heatmap() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) PseudotimeAggregationResult (class in scarf) PseudotimeMarkerResult (class in scarf) PseudotimeScoreResult (class in scarf) Q qc() (in module scarf.plotting) query_neighbors() (scarf.DataStore method) R rawData (scarf.assay.Assay attribute) read_gmt() (in module scarf) readWorkers (scarf.storage.io_policy.StorageIoPolicy attribute) reclassify_features() (scarf.readers.CrDirReader method) (scarf.readers.CrReader method) reductionArtifacts (scarf.SeuratImportResult attribute) register_theme() (in module scarf.plotting) remove_trend() (scarf.metadata.MetaData method) rename_assays() (scarf.readers.CrDirReader method) (scarf.readers.CrReader method) report() (scarf.agent.AutomatedWorkflowResult method) (scarf.PipelineRun method) Repository (class in scarf.cytebase) rescale_array() (in module scarf) reset_key() (scarf.metadata.MetaData method) resolve_features() (scarf.DataStore method) reuse RNAassay (class in scarf.assay) rolling_window() (in module scarf) run() (scarf.datastore.pipeline_accessor.PipelineAccessor method) run_aucell() (scarf.datastore.datastore.DataStore method) run_cell_cycle_scoring() (scarf.datastore.datastore.DataStore method) run_custom_reduction() (scarf.DataStore method) run_diffusion_operator() (scarf.datastore.datastore.DataStore method) run_doublet_detection() (scarf.datastore.datastore.DataStore method) run_fate_mapping() (scarf.datastore.datastore.DataStore method) run_feature_percentage() (scarf.datastore.datastore.DataStore method) run_harmony() (in module scarf.embeddings) (scarf.DataStore method) run_hto_demultiplexing() (scarf.datastore.datastore.DataStore method) run_leiden_clustering() (scarf.datastore.datastore.DataStore method) run_lsi() (scarf.DataStore method) run_mapping() (scarf.DataStore method) run_marker_search() (scarf.datastore.datastore.DataStore method) run_normalization() (scarf.DataStore method) run_paris_clustering() (scarf.datastore.datastore.DataStore method) run_pca() (scarf.DataStore method) run_pseudotime_aggregation() (scarf.datastore.datastore.DataStore method) run_pseudotime_marker_search() (scarf.datastore.datastore.DataStore method) run_pseudotime_scoring() (scarf.datastore.datastore.DataStore method) run_recipe() (in module scarf.plotting) (scarf.datastore.plot_accessor.DataStorePlotAccessor method) run_statistical_testing() (scarf.datastore.datastore.DataStore method) run_topacedo_sampler() (scarf.datastore.datastore.DataStore method) run_tsne() (scarf.datastore.datastore.DataStore method) run_umap() (scarf.datastore.datastore.DataStore method) run_waggr() (scarf.datastore.datastore.DataStore method) S save() (scarf.plotting.PlotResult method) save_provenance() (scarf.plotting.PlotResult method) scalar (scarf.assay.RNAassay attribute) scarf.logger (built-in variable) scarf.metrics module scarf.plotting module scarf.tqdm_params (built-in variable) score_features() (scarf.assay.Assay method) select_all_features() (scarf.datastore.datastore.DataStore method) select_cells() (scarf.datastore.datastore.DataStore method) select_detected_features() (scarf.datastore.datastore.DataStore method) select_hvgs() (scarf.datastore.datastore.DataStore method) select_prevalent_peaks() (scarf.datastore.datastore.DataStore method) set_default_assay() (scarf.datastore.datastore.DataStore method) set_feature_selection() (scarf.datastore.datastore.DataStore method) set_verbosity() (in module scarf) SeuratImportResult (class in scarf) SeuratInspectResult (class in scarf) SeuratReader (class in scarf) SeuratToZarr (class in scarf) sf (scarf.assay.Assay attribute) (scarf.assay.RNAassay attribute) show_zarr_tree() (scarf.datastore.datastore.DataStore method) sift() (scarf.metadata.MetaData method) silhouette_scoring() (in module scarf.metrics) SizeScale (class in scarf.plotting) smart_label() (scarf.datastore.datastore.DataStore method) snapshot_cell_selection() (scarf.DataStore method) SNN integration source_names (scarf.EnrichmentResult attribute) source_sizes (scarf.EnrichmentResult attribute) SparseToZarr (class in scarf.writers) StatisticalTestResult (class in scarf.features.statistical) storage_path (scarf.EnrichmentResult attribute) StorageIoPolicy (class in scarf.storage.io_policy) stream() (scarf.GffReader method) StudyDesign (class in scarf.plotting) subset_assay_zarr() (in module scarf.writers) SubsetZarr (class in scarf.writers) summary() (scarf.DataStore method) system_call() (in module scarf) T theme_context() (in module scarf.plotting) THEMES (in module scarf.plotting) to_anndata() (scarf.datastore.datastore.DataStore method) to_bed() (scarf.GffReader method) to_dict() (scarf.DataStoreSummary method) to_h5ad() (in module scarf.writers) to_mtx() (in module scarf.writers) to_pandas_dataframe() (scarf.metadata.MetaData method) to_raw_sparse() (scarf.assay.Assay method) TopACeDo tqdmbar() (in module scarf) U unitBytes (scarf.storage.count_matrix.CountMatrixPolicy attribute) update_key() (scarf.metadata.MetaData method) V validate_dataset_fingerprint() (scarf.MappingReference method) validate_frozen_axes() (scarf.MappingReference method) W WNN integration write_renorm_subset_to_zarr() (in module scarf.writers) writeWorkers (scarf.storage.io_policy.StorageIoPolicy attribute) Z z (scarf.assay.Assay attribute) (scarf.writers.CrToZarr attribute) (scarf.writers.CSVtoZarr attribute) (scarf.writers.H5adToZarr attribute) (scarf.writers.LoomToZarr attribute) (scarf.writers.SparseToZarr attribute) zw (scarf.datastore.datastore.DataStore property)
