Index A | C | D | F | G | H | I | L | M | N | R | S | T | U | Z A active_index() (scarf.metadata.MetaData method) add_percent_feature() (scarf.assay.Assay method) ADTassay (class in scarf.assay) Assay (class in scarf.assay) 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) autoNames (scarf.readers.CrH5Reader attribute) 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) 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 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) 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) fn (scarf.writers.CrToZarr attribute) (scarf.writers.H5adToZarr attribute) (scarf.writers.LoomToZarr attribute) (scarf.writers.NaboH5ToZarr attribute) G get_cell_attrs() (scarf.readers.LoomReader method) get_cell_columns() (scarf.readers.H5adReader method) get_dtype() (scarf.metadata.MetaData method) get_feat_columns() (scarf.readers.H5adReader method) get_feature_attrs() (scarf.readers.LoomReader method) get_index_by() (scarf.metadata.MetaData method) 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_offset (scarf.readers.CrDirReader attribute) index_to_bool() (scarf.metadata.MetaData method) insert() (scarf.metadata.MetaData method) iter_normed_feature_wise() (scarf.assay.Assay method) L 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 mark_hvgs() (scarf.assay.RNAassay method) mark_prevalent_peaks() (scarf.assay.ATACassay method) matFn (scarf.readers.CrDirReader attribute) matrix_key (scarf.readers.H5adReader attribute) matrixDtype (scarf.readers.H5adReader attribute) (scarf.readers.LoomReader attribute) matrixKey (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) mtx_separator (scarf.readers.CrDirReader attribute) 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) R rawData (scarf.assay.Assay attribute) remove_trend() (scarf.metadata.MetaData method) reset_key() (scarf.metadata.MetaData method) RNAassay (class in scarf.assay) 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) set_feature_stats() (scarf.assay.ATACassay method) (scarf.assay.RNAassay method) sf (scarf.assay.Assay attribute) (scarf.assay.RNAassay attribute) sift() (scarf.metadata.MetaData method) SubsetZarr (class in scarf.writers) T 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.writers.CrToZarr attribute) (scarf.writers.H5adToZarr attribute) (scarf.writers.LoomToZarr attribute) (scarf.writers.NaboH5ToZarr attribute) (scarf.writers.ZarrMerge attribute) ZarrMerge (class in scarf.writers)