Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X A adatas (snapatac2.AnnDataSet attribute) add_cor_scores() (in module snapatac2.tl) add_regr_scores() (in module snapatac2.tl) add_tf_binding() (in module snapatac2.tl) add_tile_matrix() (in module snapatac2.pp) aggregate_cells() (in module snapatac2.tl) aggregate_X() (in module snapatac2.tl) AnnData (class in snapatac2) AnnDataSet (class in snapatac2) annotation (in module snapatac2.genome), [1], [2], [3], [4], [5], [6], [7] (snapatac2.genome.Genome attribute) (snapatac2.genome.Genome property) B backend (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) C call_cells() (in module snapatac2.pp) chrom_sizes (in module snapatac2.genome), [1], [2], [3], [4], [5], [6], [7] (snapatac2.genome.Genome attribute) (snapatac2.genome.Genome property) chunked_X() (snapatac2.AnnData method) (snapatac2.AnnDataSet method) cis_bp() (in module snapatac2.datasets) close() (snapatac2.AnnData method) (snapatac2.AnnDataSet method) colon() (in module snapatac2.datasets) copy() (snapatac2.AnnData method) cre_HEA() (in module snapatac2.datasets) D dbscan() (in module snapatac2.tl) diff_test() (in module snapatac2.tl) E export_coverage() (in module snapatac2.ex) export_fragments() (in module snapatac2.ex) F fasta (in module snapatac2.genome), [1], [2], [3], [4], [5], [6], [7] (snapatac2.genome.Genome attribute) (snapatac2.genome.Genome property) filename (snapatac2.AnnData attribute) filter_cells() (in module snapatac2.pp) filter_doublets() (in module snapatac2.pp) frag_size_distr() (in module snapatac2.metrics) frip() (in module snapatac2.metrics) G Genome (class in snapatac2.genome) GRCh37 (in module snapatac2.genome) GRCh38 (in module snapatac2.genome) GRCm38 (in module snapatac2.genome) GRCm39 (in module snapatac2.genome) H harmony() (in module snapatac2.pp) hdbscan() (in module snapatac2.tl) hg19 (in module snapatac2.genome) hg38 (in module snapatac2.genome) I import_contacts() (in module snapatac2.pp) import_fragments() (in module snapatac2.pp) import_values() (in module snapatac2.pp) init_network_from_annotation() (in module snapatac2.tl) is_closed() (snapatac2.AnnData method) (snapatac2.AnnDataSet method) isbacked (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) K kmeans() (in module snapatac2.tl) knn() (in module snapatac2.pp) L layers (snapatac2.AnnData attribute) leiden() (in module snapatac2.tl) link_tf_to_gene() (in module snapatac2.tl) M macs3() (in module snapatac2.tl) make_fragment_file() (in module snapatac2.pp) make_gene_matrix() (in module snapatac2.pp) make_peak_matrix() (in module snapatac2.pp) marker_regions() (in module snapatac2.tl) merge_peaks() (in module snapatac2.tl) Meuleman_2020() (in module snapatac2.datasets) mm10 (in module snapatac2.genome) mm39 (in module snapatac2.genome) mnc_correct() (in module snapatac2.pp) motif_enrichment() (in module snapatac2.pl) (in module snapatac2.tl) multi_spectral() (in module snapatac2.tl) N n_obs (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) n_vars (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) network_edge_stat() (in module snapatac2.pl) O obs (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) obs_ix() (snapatac2.AnnData method) (snapatac2.AnnDataSet method) obs_names (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) obsm (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) obsp (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) open() (snapatac2.AnnData method) P pbmc10k_multiome() (in module snapatac2.datasets) pbmc500() (in module snapatac2.datasets) pbmc5k() (in module snapatac2.datasets) prune_network() (in module snapatac2.tl) R read() (in module snapatac2) read_10x_mtx() (in module snapatac2) read_dataset() (in module snapatac2) read_mtx() (in module snapatac2) recipe_10x_metrics() (in module snapatac2.pp) regions() (in module snapatac2.pl) render_plot() (in module snapatac2.pl) S scanorama_integrate() (in module snapatac2.pp) scrublet() (in module snapatac2.pp) select_features() (in module snapatac2.pp) shape (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) spectral() (in module snapatac2.tl) spectral_eigenvalues() (in module snapatac2.pl) subset() (snapatac2.AnnData method) (snapatac2.AnnDataSet method) summary_by_chrom() (in module snapatac2.metrics) T to_adata() (snapatac2.AnnDataSet method) to_memory() (snapatac2.AnnData method) tsse() (in module snapatac2.metrics) (in module snapatac2.pl) U umap() (in module snapatac2.pl) (in module snapatac2.tl) uns (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) V var (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) var_ix() (snapatac2.AnnData method) (snapatac2.AnnDataSet method) var_names (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) varm (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) varp (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute) W write() (snapatac2.AnnData method) X X (snapatac2.AnnData attribute) (snapatac2.AnnDataSet attribute)