Index A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | U | Z A active_index() (scarf.metadata.MetaData method) add_grouped_assay() (scarf.datastore.datastore.DataStore method) add_melded_assay() (scarf.datastore.datastore.DataStore method) add_percent_feature() (scarf.assay.Assay method) ADTassay (class in scarf.assay) Assay (class in scarf.assay) assay_names (scarf.datastore.base_datastore.BaseDataStore property) assayFeats (scarf.readers.CrH5Reader attribute) assayGroup (scarf.writers.ZarrMerge attribute) assayName (scarf.writers.H5adToZarr attribute) (scarf.writers.LoomToZarr attribute) (scarf.writers.NaboH5ToZarr attribute) assays (scarf.writers.ZarrMerge attribute) ATACassay (class in scarf.assay) attrs (scarf.assay.Assay attribute) auto_filter_cells() (scarf.datastore.datastore.DataStore method) autoNames (scarf.readers.CrH5Reader attribute) B BaseDataStore (class in scarf.datastore.base_datastore) C catNamesKey (scarf.readers.H5adReader attribute) cell_ids() (scarf.readers.H5adReader method) (scarf.readers.LoomReader method) (scarf.readers.NaboH5Reader method) cell_names() (scarf.readers.LoomReader method) cellAttrsKey (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) cellIdsKey (scarf.readers.H5adReader attribute) cellNamesKey (scarf.readers.LoomReader attribute) cells (scarf.assay.Assay attribute) (scarf.datastore.base_datastore.BaseDataStore attribute) (scarf.datastore.graph_datastore.GraphDataStore attribute) chunkSizes (scarf.writers.CrToZarr attribute) (scarf.writers.H5adToZarr attribute) (scarf.writers.LoomToZarr attribute) (scarf.writers.NaboH5ToZarr attribute) close() (scarf.readers.CrH5Reader method) columns (scarf.metadata.MetaData property) consume() (scarf.readers.CrDirReader method) (scarf.readers.CrH5Reader method) (scarf.readers.H5adReader method) (scarf.readers.LoomReader method) (scarf.readers.NaboH5Reader method) consume_dataset() (scarf.readers.H5adReader method) consume_group() (scarf.readers.H5adReader method) cr (scarf.writers.CrToZarr attribute) CrDirReader (class in scarf.readers) CrH5Reader (class in scarf.readers) CrToZarr (class in scarf.writers) D DataStore (class in scarf.datastore.datastore) drop() (scarf.metadata.MetaData method) dump() (scarf.writers.CrToZarr method) (scarf.writers.H5adToZarr method) (scarf.writers.LoomToZarr method) (scarf.writers.NaboH5ToZarr method) (scarf.writers.ZarrMerge method) E export_markers_to_csv() (scarf.datastore.datastore.DataStore method) F feat_ids() (scarf.readers.H5adReader method) (scarf.readers.NaboH5Reader method) feat_names() (scarf.readers.H5adReader method) (scarf.readers.NaboH5Reader method) featCollection (scarf.writers.ZarrMerge attribute) featIdsKey (scarf.readers.H5adReader attribute) featNamesKey (scarf.readers.H5adReader attribute) featOrder (scarf.writers.ZarrMerge attribute) feats (scarf.assay.Assay attribute) feature_ids() (scarf.readers.LoomReader method) feature_names() (scarf.readers.LoomReader method) featureAttrsKey (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) featureIdsKey (scarf.readers.LoomReader attribute) featureNamesKey (scarf.readers.LoomReader attribute) fetch() (scarf.metadata.MetaData method) fetch_all() (scarf.metadata.MetaData method) filter_cells() (scarf.datastore.datastore.DataStore method) fn (scarf.writers.LoomToZarr attribute) (scarf.writers.NaboH5ToZarr attribute) G get_cell_attrs() (scarf.readers.LoomReader method) get_cell_columns() (scarf.readers.H5adReader method) get_cell_vals() (scarf.datastore.base_datastore.BaseDataStore method) get_dtype() (scarf.metadata.MetaData method) get_feat_columns() (scarf.readers.H5adReader method) get_feature_attrs() (scarf.readers.LoomReader method) get_imputed() (scarf.datastore.graph_datastore.GraphDataStore method) get_index_by() (scarf.metadata.MetaData method) get_mapping_score() (scarf.datastore.mapping_datastore.MappingDatastore method) get_markers() (scarf.datastore.datastore.DataStore method) get_target_classes() (scarf.datastore.mapping_datastore.MappingDatastore method) GraphDataStore (class in scarf.datastore.graph_datastore) grep() (scarf.metadata.MetaData method) groupCodes (scarf.readers.H5adReader attribute) grp (scarf.readers.CrH5Reader attribute) grpNames (scarf.readers.CrH5Reader attribute) H h5 (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) (scarf.readers.NaboH5Reader attribute) (scarf.writers.NaboH5ToZarr attribute) h5ad (scarf.writers.H5adToZarr attribute) H5adReader (class in scarf.readers) H5adToZarr (class in scarf.writers) h5obj (scarf.readers.CrH5Reader attribute) head() (scarf.metadata.MetaData method) I index (scarf.metadata.MetaData attribute) index_to_bool() (scarf.metadata.MetaData method) indexOffset (scarf.readers.CrDirReader attribute) insert() (scarf.metadata.MetaData method) integrate_assays() (scarf.datastore.graph_datastore.GraphDataStore method) iter_normed_feature_wise() (scarf.assay.Assay method) L load_graph() (scarf.datastore.graph_datastore.GraphDataStore method) load_unified_graph() (scarf.datastore.mapping_datastore.MappingDatastore method) loc (scarf.readers.CrDirReader attribute) locations (scarf.metadata.MetaData attribute) loom (scarf.writers.LoomToZarr attribute) LoomReader (class in scarf.readers) LoomToZarr (class in scarf.writers) M make_bulk() (scarf.datastore.datastore.DataStore method) make_graph() (scarf.datastore.graph_datastore.GraphDataStore method) MappingDatastore (class in scarf.datastore.mapping_datastore) mark_hvgs() (scarf.assay.RNAassay method) (scarf.datastore.datastore.DataStore method) mark_prevalent_peaks() (scarf.assay.ATACassay method) (scarf.datastore.datastore.DataStore method) matFn (scarf.readers.CrDirReader attribute) matrixDtype (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) matrixKey (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) mergedCells (scarf.writers.ZarrMerge attribute) mergedFeats (scarf.writers.ZarrMerge attribute) MetaData (class in scarf.metadata) mount_location() (scarf.metadata.MetaData method) multi_sift() (scarf.metadata.MetaData method) N N (scarf.metadata.MetaData attribute) NaboH5Reader (class in scarf.readers) NaboH5ToZarr (class in scarf.writers) name (scarf.assay.Assay attribute) names (scarf.writers.ZarrMerge attribute) nCells (scarf.readers.CrH5Reader attribute) (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) (scarf.readers.NaboH5Reader attribute) (scarf.writers.ZarrMerge attribute) nFeats (scarf.writers.ZarrMerge attribute) nFeatures (scarf.readers.CrH5Reader attribute) (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) (scarf.readers.NaboH5Reader attribute) 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) nthreads (scarf.assay.Assay attribute) (scarf.datastore.base_datastore.BaseDataStore attribute) (scarf.datastore.graph_datastore.GraphDataStore attribute) P plot_cells_dists() (scarf.datastore.datastore.DataStore method) plot_cluster_tree() (scarf.datastore.datastore.DataStore method) plot_layout() (scarf.datastore.datastore.DataStore method) plot_marker_heatmap() (scarf.datastore.datastore.DataStore method) plot_pseudotime_heatmap() (scarf.datastore.datastore.DataStore method) plot_unified_layout() (scarf.datastore.mapping_datastore.MappingDatastore method) R rawData (scarf.assay.Assay attribute) remove_trend() (scarf.metadata.MetaData method) reset_key() (scarf.metadata.MetaData method) RNAassay (class in scarf.assay) run_cell_cycle_scoring() (scarf.datastore.datastore.DataStore method) run_clustering() (scarf.datastore.graph_datastore.GraphDataStore method) run_leiden_clustering() (scarf.datastore.graph_datastore.GraphDataStore method) run_mapping() (scarf.datastore.mapping_datastore.MappingDatastore method) run_marker_search() (scarf.datastore.datastore.DataStore method) run_pseudotime_aggregation() (scarf.datastore.datastore.DataStore method) run_pseudotime_marker_search() (scarf.datastore.datastore.DataStore method) run_pseudotime_scoring() (scarf.datastore.graph_datastore.GraphDataStore method) run_topacedo_sampler() (scarf.datastore.graph_datastore.GraphDataStore method) run_tsne() (scarf.datastore.graph_datastore.GraphDataStore method) run_umap() (scarf.datastore.graph_datastore.GraphDataStore method) run_unified_tsne() (scarf.datastore.mapping_datastore.MappingDatastore method) run_unified_umap() (scarf.datastore.mapping_datastore.MappingDatastore method) S save_aggregated_ordering() (scarf.assay.Assay method) save_normalized_data() (scarf.assay.Assay method) save_normed_for_query() (scarf.assay.Assay method) scalar (scarf.assay.RNAassay attribute) score_features() (scarf.assay.Assay method) sep (scarf.readers.CrDirReader attribute) set_default_assay() (scarf.datastore.base_datastore.BaseDataStore method) set_feature_stats() (scarf.assay.ATACassay method) (scarf.assay.RNAassay method) sf (scarf.assay.Assay attribute) (scarf.assay.RNAassay attribute) show_zarr_tree() (scarf.datastore.datastore.DataStore method) sift() (scarf.metadata.MetaData method) smart_label() (scarf.datastore.datastore.DataStore method) SubsetZarr (class in scarf.writers) T to_anndata() (scarf.datastore.datastore.DataStore method) to_pandas_dataframe() (scarf.metadata.MetaData method) to_raw_sparse() (scarf.assay.Assay method) to_sparse() (scarf.readers.CrDirReader method) U unmount_location() (scarf.metadata.MetaData method) update_key() (scarf.metadata.MetaData method) Z z (scarf.assay.Assay attribute) (scarf.datastore.base_datastore.BaseDataStore attribute) (scarf.datastore.graph_datastore.GraphDataStore attribute) (scarf.writers.CrToZarr attribute) (scarf.writers.H5adToZarr attribute) (scarf.writers.LoomToZarr attribute) (scarf.writers.NaboH5ToZarr attribute) (scarf.writers.ZarrMerge attribute) ZarrMerge (class in scarf.writers)