Index A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | U | W | Z A adapter_max_edits (smftools.informatics.bam_functions.UMIKitConfig attribute) adapter_pad (smftools.informatics.bam_functions.FlankingConfig attribute) adapter_side (smftools.informatics.bam_functions.FlankingConfig attribute) add_demux_type_annotation() (in module smftools.informatics.h5ad_functions) add_demux_type_from_bm_tag() (in module smftools.informatics.h5ad_functions) add_ep_obs_columns() (in module smftools.analysis.compute.ep_classification) add_read_length_and_mapping_qc() (in module smftools.informatics.h5ad_functions) add_read_tag_annotations() (in module smftools.informatics.h5ad_functions) add_secondary_supplementary_alignment_flags() (in module smftools.informatics.h5ad_functions) align_and_sort_BAM() (in module smftools.informatics.bam_functions) aligned_BAM_to_bed() (in module smftools.informatics.bed_functions) amplicon_max_edits (smftools.informatics.bam_functions.UMIKitConfig attribute) amplicon_pad (smftools.informatics.bam_functions.FlankingConfig attribute) amplicon_side (smftools.informatics.bam_functions.FlankingConfig attribute) analyze_autocorr_matrix() (in module smftools.tools.spatial_autocorrelation) analyze_fft_periodicity() (in module smftools.analysis.compute.ls_periodicity) analyze_ls_periodicity() (in module smftools.analysis.compute.ls_periodicity) analyze_ls_periodicity_direct() (in module smftools.analysis.compute.ls_periodicity) annotate_demux_type_from_bi_tag() (in module smftools.informatics.bam_functions) annotate_pod5_origin() (in module smftools.informatics.h5ad_functions) annotate_umi_tags_in_bam() (in module smftools.informatics.bam_functions) append_base_context() (in module smftools.preprocessing) append_binary_layer_by_base_context() (in module smftools.preprocessing) append_reference_strand_quality_stats() (in module smftools.informatics.h5ad_functions) B bam_qc() (in module smftools.informatics.bam_functions) barcode_amplicon_gap_tolerance (smftools.informatics.bam_functions.BarcodeKitConfig attribute) barcode_composite_max_edits (smftools.informatics.bam_functions.BarcodeKitConfig attribute) barcode_ends (smftools.informatics.bam_functions.BarcodeKitConfig attribute) barcode_length (smftools.informatics.bam_functions.BarcodeKitConfig attribute) barcode_max_edit_distance (smftools.informatics.bam_functions.BarcodeKitConfig attribute) barcode_min_separation (smftools.informatics.bam_functions.BarcodeKitConfig attribute) BarcodeKitConfig (class in smftools.informatics.bam_functions) barcodes (smftools.informatics.bam_functions.BarcodeKitConfig attribute) basecall_pod5s() (in module smftools.informatics.pod5_functions) binarize_adata() (in module smftools.preprocessing.binarize) binarize_converted_base_identities() (in module smftools.informatics.binarize_converted_base_identities) binarize_on_Youden() (in module smftools.preprocessing) binary_autocorrelation_with_spacing() (in module smftools.analysis.compute.autocorrelation) (in module smftools.tools.read_stats) (in module smftools.tools.spatial_autocorrelation) binary_layers_to_ohe() (in module smftools.preprocessing.binary_layers_to_ohe) bootstrap_periodicity() (in module smftools.tools.spatial_autocorrelation) build_barcode_index() (in module smftools.analysis.compute.read_cache) build_barcode_sidecar_from_split_bams() (in module smftools.informatics.bam_functions) build_classified_read_set() (in module smftools.informatics.bam_functions) build_obs_mask() (in module smftools.analysis.filters.obs_filters) build_position_mask() (in module smftools.analysis.filters.position_filters) C cache_dir() (in module smftools.analysis.compute.read_cache) cache_key() (in module smftools.analysis.compute.read_cache) calculate_complexity_II() (in module smftools.preprocessing) calculate_consensus() (in module smftools.preprocessing.calculate_consensus) calculate_coverage() (in module smftools.preprocessing) calculate_pairwise_differences() (in module smftools.preprocessing.calculate_pairwise_differences) calculate_pairwise_hamming_distances() (in module smftools.preprocessing.calculate_pairwise_hamming_distances) calculate_position_Youden() (in module smftools.preprocessing) calculate_read_length_stats() (in module smftools.preprocessing) calculate_read_modification_stats() (in module smftools.preprocessing) calculate_relative_risk_on_activity() (in module smftools.tools.position_stats) calculate_row_entropy() (in module smftools.tools.read_stats) calculate_umap() (in module smftools.tools) canoncall() (in module smftools.informatics.basecalling) classify_position() (in module smftools.analysis.compute.ep_classification) clean_NaN() (in module smftools.preprocessing) cluster_adata_on_methylation() (in module smftools.tools) cluster_from_pca() (in module smftools.analysis.compute.dimensionality_reduction) combine_layers() (in module smftools.tools.general_tools) complement_base_list() (in module smftools.informatics.complement_base_list) compute_positionwise_statistics() (in module smftools.tools.position_stats) compute_replicate_curve() (in module smftools.analysis.compute.autocorrelation) compute_single_molecule_periodicity() (in module smftools.analysis.compute.autocorrelation) compute_single_molecule_periodicity_direct() (in module smftools.analysis.compute.autocorrelation) concatenate_fastqs_to_bam() (in module smftools.informatics.bam_functions) converted_BAM_to_adata() (in module smftools.informatics) count_aligned_reads() (in module smftools.informatics.bam_functions) coverage_filter() (in module smftools.analysis.compute.dimensionality_reduction) create_nan_mask_from_X() (in module smftools.tools.general_tools) create_nan_or_non_gpc_mask() (in module smftools.tools.general_tools) D dCas9_kinetics() (in module smftools.datasets.datasets) demux_and_index_BAM() (in module smftools.informatics.bam_functions) derive_bm_from_bi_to_sidecar() (in module smftools.informatics.bam_functions) derive_umi_orientation_tags_from_aligned_bam() (in module smftools.informatics.bam_functions) E estimate_snr() (in module smftools.tools.spatial_autocorrelation) expand_bi_tag_columns() (in module smftools.informatics.h5ad_functions) extract_and_assign_barcodes_in_bam() (in module smftools.informatics.bam_functions) extract_base_identities() (in module smftools.informatics.bam_functions) extract_intervals_from_row() (in module smftools.analysis.compute.hmm_features) extract_mods() (in module smftools.informatics.modkit_functions) extract_read_features_from_bam() (in module smftools.informatics.bam_functions) extract_read_lengths_from_bed() (in module smftools.informatics.bed_functions) extract_read_tags_from_bam() (in module smftools.informatics.bam_functions) extract_readnames_from_bam() (in module smftools.informatics.bam_functions) extract_secondary_supplementary_alignment_spans() (in module smftools.informatics.bam_functions) F fast5_to_pod5() (in module smftools.informatics.pod5_functions) filter_adata_by_nan_proportion() (in module smftools.preprocessing) filter_reads_on_length_quality_mapping() (in module smftools.preprocessing) filter_reads_on_modification_thresholds() (in module smftools.preprocessing) find_conversion_sites() (in module smftools.informatics.fasta_functions) find_peak_in_nrl_band() (in module smftools.tools.spatial_autocorrelation) find_peak_ls() (in module smftools.analysis.compute.ls_periodicity) find_secondary_supplementary_read_names() (in module smftools.informatics.bam_functions) fit_exponential_envelope() (in module smftools.tools.spatial_autocorrelation) flag_duplicate_reads() (in module smftools.preprocessing) flank_seq (smftools.informatics.bam_functions.UMIExtractionResult attribute) flanking (smftools.informatics.bam_functions.BarcodeKitConfig attribute) (smftools.informatics.bam_functions.UMIKitConfig attribute) FlankingConfig (class in smftools.informatics.bam_functions) fwhm_freq_to_bp() (in module smftools.tools.spatial_autocorrelation) fwhm_ls() (in module smftools.analysis.compute.ls_periodicity) G gaussian_fit_plot() (in module smftools.analysis.plot.histograms) generate_converted_FASTA() (in module smftools.informatics.fasta_functions) get_chromosome_lengths() (in module smftools.informatics.fasta_functions) get_native_references() (in module smftools.informatics.fasta_functions) I import_HERE() (in module smftools.datasets.datasets) index_fasta() (in module smftools.informatics.fasta_functions) invert_adata() (in module smftools.preprocessing) is_cached() (in module smftools.analysis.compute.read_cache) K Kissiov_and_McKenna_2025() (in module smftools.datasets.datasets) L left_ref_end (smftools.informatics.bam_functions.PerEndFlankingConfig attribute) length (smftools.informatics.bam_functions.UMIKitConfig attribute) load_barcode_index() (in module smftools.analysis.compute.read_cache) load_barcode_references_from_yaml() (in module smftools.informatics.bam_functions) load_layer() (in module smftools.analysis.compute.read_cache) load_obs_metadata() (in module smftools.analysis.compute.read_cache) load_sample_sheet() (in module smftools.preprocessing) load_umi_config_from_yaml() (in module smftools.informatics.bam_functions) load_var_info() (in module smftools.analysis.compute.read_cache) load_zarr_layer() (in module smftools.analysis.compute.read_cache) load_zarr_obs() (in module smftools.analysis.compute.read_cache) load_zarr_var() (in module smftools.analysis.compute.read_cache) load_zarr_var_fast() (in module smftools.analysis.compute.read_cache) ls_periodogram_from_autocorr() (in module smftools.analysis.compute.ls_periodicity) ls_periodogram_from_signal() (in module smftools.analysis.compute.ls_periodicity) M make_dirs() (in module smftools.preprocessing.make_dirs) make_features_acf() (in module smftools.analysis.compute.dimensionality_reduction) make_features_raw() (in module smftools.analysis.compute.dimensionality_reduction) make_modbed() (in module smftools.informatics.modkit_functions) make_ticks() (in module smftools.analysis.compute.pearson) max_cigar_deletion() (in module smftools.analysis.filters.obs_filters) min_non_diagonal() (in module smftools.preprocessing.min_non_diagonal) modcall() (in module smftools.informatics.basecalling) modkit_extract_to_adata() (in module smftools.informatics) modQC() (in module smftools.informatics.modkit_functions) module smftools.analysis.compute.autocorrelation smftools.analysis.compute.dimensionality_reduction smftools.analysis.compute.ep_classification smftools.analysis.compute.hmm_features smftools.analysis.compute.ls_periodicity smftools.analysis.compute.pearson smftools.analysis.compute.read_cache smftools.analysis.config.hmm_histogram smftools.analysis.filters.obs_filters smftools.analysis.filters.position_filters smftools.analysis.plot.autocorr smftools.analysis.plot.heatmaps smftools.analysis.plot.histograms smftools.analysis.plot.locus smftools.datasets smftools.datasets.datasets smftools.informatics smftools.informatics.bam_functions smftools.informatics.basecalling smftools.informatics.bed_functions smftools.informatics.binarize_converted_base_identities smftools.informatics.complement_base_list smftools.informatics.fasta_functions smftools.informatics.h5ad_functions smftools.informatics.modkit_functions smftools.informatics.ohe smftools.informatics.pod5_functions smftools.preprocessing smftools.preprocessing.binarize smftools.preprocessing.binary_layers_to_ohe smftools.preprocessing.calculate_consensus smftools.preprocessing.calculate_pairwise_differences smftools.preprocessing.calculate_pairwise_hamming_distances smftools.preprocessing.make_dirs smftools.preprocessing.min_non_diagonal smftools.preprocessing.recipes smftools.tools smftools.tools.general_tools smftools.tools.position_stats smftools.tools.read_stats smftools.tools.spatial_autocorrelation N name (smftools.informatics.bam_functions.BarcodeKitConfig attribute) nan_pearson_matrix() (in module smftools.analysis.compute.pearson) O ohe_batching() (in module smftools.informatics.ohe) ohe_layers_decode() (in module smftools.informatics.ohe) one_hot_decode() (in module smftools.informatics.ohe) one_hot_encode() (in module smftools.informatics.ohe) open_zarr_cache() (in module smftools.analysis.compute.read_cache) P PerEndFlankingConfig (class in smftools.informatics.bam_functions) plot_autocorr_overlay() (in module smftools.analysis.plot.autocorr) plot_interval_histogram() (in module smftools.analysis.plot.histograms) plot_ls_overlay() (in module smftools.analysis.plot.autocorr) plot_metric_barplot_paired() (in module smftools.analysis.plot.autocorr) plot_metric_histogram() (in module smftools.analysis.plot.autocorr) plot_pearson_heatmap() (in module smftools.analysis.plot.heatmaps) plot_positionwise_matrices() (in module smftools.tools.position_stats) plot_sm_periodogram_overlay() (in module smftools.analysis.plot.autocorr) psd_from_autocorr() (in module smftools.analysis.compute.ls_periodicity) (in module smftools.tools.spatial_autocorrelation) R random_fill_nans() (in module smftools.tools.position_stats) (in module smftools.tools.read_stats) (in module smftools.tools.spatial_autocorrelation) recipe_1_Kissiov_and_McKenna_2025() (in module smftools.preprocessing.recipes) recipe_2_Kissiov_and_McKenna_2025() (in module smftools.preprocessing.recipes) reindex_references_adata() (in module smftools.preprocessing) resolve_barcode_config() (in module smftools.informatics.bam_functions) resolve_barcode_str() (in module smftools.analysis.compute.read_cache) resolve_umi_config() (in module smftools.informatics.bam_functions) right_ref_end (smftools.informatics.bam_functions.PerEndFlankingConfig attribute) rolling_autocorr_metrics() (in module smftools.tools.spatial_autocorrelation) rolling_mean_nan() (in module smftools.analysis.compute.ls_periodicity) rolling_smooth() (in module smftools.analysis.plot.autocorr) run_multiqc() (in module smftools.informatics) run_pipeline() (in module smftools.analysis.compute.dimensionality_reduction) S same_orientation (smftools.informatics.bam_functions.PerEndFlankingConfig attribute) (smftools.informatics.bam_functions.UMIKitConfig attribute) sample_autocorr_at_harmonics() (in module smftools.tools.spatial_autocorrelation) separate_bam_by_bc() (in module smftools.informatics.bam_functions) slot (smftools.informatics.bam_functions.UMIExtractionResult attribute) smftools.analysis.compute.autocorrelation module smftools.analysis.compute.dimensionality_reduction module smftools.analysis.compute.ep_classification module smftools.analysis.compute.hmm_features module smftools.analysis.compute.ls_periodicity module smftools.analysis.compute.pearson module smftools.analysis.compute.read_cache module smftools.analysis.config.hmm_histogram module smftools.analysis.filters.obs_filters module smftools.analysis.filters.position_filters module smftools.analysis.plot.autocorr module smftools.analysis.plot.heatmaps module smftools.analysis.plot.histograms module smftools.analysis.plot.locus module smftools.datasets module smftools.datasets.datasets module smftools.informatics module smftools.informatics.bam_functions module smftools.informatics.basecalling module smftools.informatics.bed_functions module smftools.informatics.binarize_converted_base_identities module smftools.informatics.complement_base_list module smftools.informatics.fasta_functions module smftools.informatics.h5ad_functions module smftools.informatics.modkit_functions module smftools.informatics.ohe module smftools.informatics.pod5_functions module smftools.preprocessing module smftools.preprocessing.binarize module smftools.preprocessing.binary_layers_to_ohe module smftools.preprocessing.calculate_consensus module smftools.preprocessing.calculate_pairwise_differences module smftools.preprocessing.calculate_pairwise_hamming_distances module smftools.preprocessing.make_dirs module smftools.preprocessing.min_non_diagonal module smftools.preprocessing.recipes module smftools.tools module smftools.tools.general_tools module smftools.tools.position_stats module smftools.tools.read_stats module smftools.tools.spatial_autocorrelation module snr_ls() (in module smftools.analysis.compute.ls_periodicity) split_and_index_BAM() (in module smftools.informatics.bam_functions) subsample_adata() (in module smftools.preprocessing) subsample_fasta_from_bed() (in module smftools.informatics.fasta_functions) subsample_pod5() (in module smftools.informatics.pod5_functions) subsample_pod5_for_basecalling() (in module smftools.informatics.pod5_functions) subsample_split_bams() (in module smftools.informatics.bam_functions) subset_adata() (in module smftools.tools) T tqdm_joblib() (in module smftools.tools.position_stats) U umap_from_pca() (in module smftools.analysis.compute.dimensionality_reduction) umi_ends (smftools.informatics.bam_functions.UMIKitConfig attribute) umi_flank_mode (smftools.informatics.bam_functions.UMIKitConfig attribute) umi_seq (smftools.informatics.bam_functions.UMIExtractionResult attribute) UMIExtractionResult (class in smftools.informatics.bam_functions) UMIKitConfig (class in smftools.informatics.bam_functions) W weighted_mean_autocorr() (in module smftools.analysis.compute.autocorrelation) (in module smftools.tools.spatial_autocorrelation) write_zarr_cache() (in module smftools.analysis.compute.read_cache) Z zarr_cache_exists() (in module smftools.analysis.compute.read_cache) zarr_index_path() (in module smftools.analysis.compute.read_cache)