LICENSE
README.md
pyproject.toml
ema/__init__.py
ema/__main__.py
ema/config.py
ema/downstream_runner.py
ema/logging_config.py
ema/main.py
ema/matrixfilter.py
ema/outputs.py
ema/progress.py
ema/provenance.py
ema/reannotate.py
ema/annotate/__init__.py
ema/annotate/annotate.py
ema/annotate/find_close.py
ema/annotate/gtf2isoform_utr.py
ema/annotate/gtf_cache.py
ema/annotate/gtftobed.py
ema/benchmark/__init__.py
ema/benchmark/cross_experiment.py
ema/benchmark/length_compare.py
ema/benchmark/metrics.py
ema/benchmark/report.py
ema/benchmark/runner.py
ema/benchmark/sweep_analysis.py
ema/benchmark/switch_diff_compare.py
ema/benchmark/visualize.py
ema/celltype/__init__.py
ema/celltype/scoring.py
ema/cli/__init__.py
ema/cli/collapse.py
ema/cli/common.py
ema/cli/config_schema.py
ema/cli/defaults.py
ema/cli/merge.py
ema/cli/parse_gtf.py
ema/cli/reannotate.py
ema/cli/run.py
ema/cli/switch.py
ema/cli/switch_combine.py
ema/cli/switch_diff.py
ema/cli/switch_geneview.py
ema/cli/switch_length.py
ema/cli/switch_match.py
ema/cli/switch_trend.py
ema/cli/wizard.py
ema/cli/yaml_loader.py
ema/clustering/__init__.py
ema/clustering/_builtins.py
ema/clustering/clustering.py
ema/clustering/evaluation.py
ema/clustering/registry.py
ema/clustering/cross_dataset/__init__.py
ema/clustering/cross_dataset/base.py
ema/clustering/cross_dataset/jaccard.py
ema/clustering/cross_dataset/marker_overlap.py
ema/clustering/cross_dataset/mnn.py
ema/clustering/cross_dataset/roundtrip.py
ema/clustering/strategies/__init__.py
ema/clustering/strategies/base.py
ema/clustering/strategies/external.py
ema/clustering/strategies/leiden_libsize.py
ema/clustering/strategies/leiden_tfidf.py
ema/countmatrix/__init__.py
ema/countmatrix/bam_utils.py
ema/countmatrix/cb_encode.py
ema/countmatrix/chrom_parallel.py
ema/countmatrix/cleavage_offset.py
ema/countmatrix/dynamic_threshold.py
ema/countmatrix/indexing.py
ema/countmatrix/pas_features.py
ema/countmatrix/pas_score.py
ema/countmatrix/pasfind.py
ema/countmatrix/paswrite.py
ema/countmatrix/peackcalling.py
ema/countmatrix/peak.py
ema/countmatrix/peak_pipeline.py
ema/countmatrix/peak_state.py
ema/countmatrix/polya.py
ema/countmatrix/read.py
ema/countmatrix/tile_runner.py
ema/countmatrix/models/pas_score_model_prime1.json
ema/data/__init__.py
ema/data/run.py
ema/datasets/__init__.py
ema/datasets/atlas_annotate.py
ema/datasets/atlas_snap.py
ema/datasets/collapse.py
ema/datasets/manager.py
ema/datasets/pas_merge.py
ema/experimental/__init__.py
ema/experimental/internal_priming.py
ema/experimental/peak_filters.py
ema/merge_bam/__init__.py
ema/merge_bam/merge.py
ema/merge_bam/runner.py
ema/quantification/__init__.py
ema/quantification/marker_selector.py
ema/quantification/pas_to_isoform.py
ema/quantification/pdui.py
ema/quantification/strategies/__init__.py
ema/quantification/strategies/base.py
ema/quantification/strategies/classic.py
ema/quantification/strategies/proportion.py
ema/quantification/strategies/shannon.py
ema/statistics/__init__.py
ema/statistics/background.py
ema/statistics/significance.py
ema/strategies/__init__.py
ema/strategies/base.py
ema/strategies/clip_seeded.py
ema/strategies/lambda_gradient.py
ema/strategies/lambda_poisson.py
ema/strategies/original.py
ema/strategies/sierra_iterative.py
ema/strategies/utils.py
ema/switch_test/__init__.py
ema/switch_test/combine.py
ema/switch_test/fishertest.py
ema/switch_test/groupby.py
ema/switch_test/long_output.py
ema/switch_test/pair_runner.py
ema/switch_test/prefilter.py
ema/switch_test/runner.py
ema/switch_test/trend.py
ema/switch_test/strategies/__init__.py
ema/switch_test/strategies/base.py
ema/switch_test/strategies/fisher.py
ema/switch_test/strategies/nb_multi.py
ema/switch_test/strategies/nb_pairwise.py
ema/utils/__init__.py
ema/utils/resource_manager.py
ema/validation/__init__.py
ema/validation/db_compare.py
ema/validation/output_validator.py
ema/validation/regression.py
ema/viz/__init__.py
ema/viz/_gene_track_helpers.py
ema/viz/_io.py
ema/viz/_meta.py
ema/viz/atlas_snap_diag_matplotlib.py
ema/viz/atlas_snap_diag_plotly.py
ema/viz/base.py
ema/viz/cluster_match_sankey_matplotlib.py
ema/viz/cluster_match_sankey_plotly.py
ema/viz/cluster_sizes_matplotlib.py
ema/viz/cluster_sizes_plotly.py
ema/viz/diff_agreement_matplotlib.py
ema/viz/diff_agreement_plotly.py
ema/viz/entropy_distribution_matplotlib.py
ema/viz/entropy_distribution_plotly.py
ema/viz/gene_track_matplotlib.py
ema/viz/gene_track_plotly.py
ema/viz/length_shifts_matplotlib.py
ema/viz/length_shifts_plotly.py
ema/viz/match_confidence_matplotlib.py
ema/viz/match_confidence_plotly.py
ema/viz/pas_overlap_matplotlib.py
ema/viz/pas_overlap_plotly.py
ema/viz/pdui_distribution_matplotlib.py
ema/viz/pdui_distribution_plotly.py
ema/viz/pdui_distribution_scanpy.py
ema/viz/peak_qc_matplotlib.py
ema/viz/peak_qc_plotly.py
ema/viz/pipeline_hooks.py
ema/viz/proportion_heatmap_matplotlib.py
ema/viz/proportion_heatmap_plotly.py
ema/viz/resource_timeline_matplotlib.py
ema/viz/resource_timeline_plotly.py
ema/viz/run_report.py
ema/viz/tile_timing_matplotlib.py
ema/viz/tile_timing_plotly.py
ema/viz/umap_matplotlib.py
ema/viz/umap_plotly.py
ema/viz/umap_scanpy.py
ema/viz/volcano_matplotlib.py
ema/viz/volcano_plotly.py
peakatail.egg-info/PKG-INFO
peakatail.egg-info/SOURCES.txt
peakatail.egg-info/dependency_links.txt
peakatail.egg-info/entry_points.txt
peakatail.egg-info/requires.txt
peakatail.egg-info/top_level.txt
test/test_cli.py
test/test_filtermatrix.py
test/test_peak.py
test/test_switch_diff_cells_mode.py
test/testconfig.py
tests/test_annotate_runscoped_b2.py
tests/test_artifact_naming_d7.py
tests/test_atlas_annotate_overlay.py
tests/test_atlas_snap_annotate_d9.py
tests/test_atlas_snap_ledger_e3.py
tests/test_atlas_snap_rate_d1.py
tests/test_atlas_snap_summit.py
tests/test_audit_cli_coverage.py
tests/test_benchmark_point_strand.py
tests/test_between_utr_report_gating_i94.py
tests/test_build_count_dfs_which.py
tests/test_canonical_roundtrip_b6.py
tests/test_cb_encode.py
tests/test_cellranger_input_compat.py
tests/test_celltype_scoring_a1.py
tests/test_changelog_section.py
tests/test_chrom_parallel_identity.py
tests/test_classic_pdui_vectorized.py
tests/test_cleavage_offset_i72.py
tests/test_cleavage_offset_prime.py
tests/test_cleavage_offset_skips_clip_supported.py
tests/test_cli_merge_parse_gtf.py
tests/test_cli_rename_peakatail.py
tests/test_cli_root.py
tests/test_cli_run.py
tests/test_cli_switch.py
tests/test_cli_wizard.py
tests/test_clip_rate_sampling.py
tests/test_cluster_matching.py
tests/test_clustering_registry.py
tests/test_collapse_a4.py
tests/test_config_schema.py
tests/test_config_schema_atlas_ip_mode_d9.py
tests/test_data_run_e4.py
tests/test_docs_consistency.py
tests/test_downstream_parallel.py
tests/test_dynamic_threshold_bounds.py
tests/test_filtered_cb_b3.py
tests/test_findings_long_e5.py
tests/test_fisher_percell_d4.py
tests/test_gene_id_repair_b7.py
tests/test_gene_track_regions.py
tests/test_global_pool.py
tests/test_gtf2isoform_utr.py
tests/test_gtf_cache_global.py
tests/test_internal_priming_strand.py
tests/test_ip_annot_filter_d6.py
tests/test_ip_filter_default.py
tests/test_label_independent_prefilter_i94.py
tests/test_logging_config.py
tests/test_marker_selector_dtype.py
tests/test_marker_top_n_double_dip_i94.py
tests/test_marker_top_n_utr_denominator_i94.py
tests/test_matrix_pas_id_row_alignment.py
tests/test_matrixfilter_vectorized.py
tests/test_nb_multi_split_d5.py
tests/test_nb_offset_full_matrix_i94.py
tests/test_nb_regression.py
tests/test_outputs_atomic_writers.py
tests/test_outputs_concat_beds.py
tests/test_pair_parallel.py
tests/test_pas_features.py
tests/test_pas_gene_artifacts_atomic_write.py
tests/test_pas_gene_overlapping_loci_i99.py
tests/test_pas_gene_rescue.py
tests/test_pas_merge.py
tests/test_pas_merge_strand_b1.py
tests/test_pas_score.py
tests/test_pas_to_isoform.py
tests/test_pas_to_isoform_spliced_dedup.py
tests/test_pas_uid_e1.py
tests/test_pasbed_status_columns_d9.py
tests/test_pdui_strategies.py
tests/test_peakcall_grid_ip_dedup.py
tests/test_polya_clip_evidence_units.py
tests/test_polya_clip_site.py
tests/test_polya_clustering.py
tests/test_polya_three_path_agreement.py
tests/test_polya_tier1_counts.py
tests/test_polya_two_tier_integration.py
tests/test_prime_compat_flags.py
tests/test_prime_dynamic_threshold_clamp.py
tests/test_prime_ip_default_mode.py
tests/test_prime_ip_escape_docs.py
tests/test_prime_sidecar_merge_guard.py
tests/test_prime_strand_implant.py
tests/test_prime_v2_compat_golden.py
tests/test_progress.py
tests/test_provenance.py
tests/test_provenance_atlas_ip_d9.py
tests/test_provenance_invariant_e3.py
tests/test_provenance_reconcile_e3.py
tests/test_provenance_wiring_e3.py
tests/test_pyproject_install.py
tests/test_ram_adaptive_tile.py
tests/test_read_check_fastpath.py
tests/test_read_geometry.py
tests/test_reannotate_cmd.py
tests/test_reannotate_out_dir_guard.py
tests/test_region_fetch.py
tests/test_release_packaging.py
tests/test_repair_gene_id.py
tests/test_resource_manager.py
tests/test_rg_sample_id_bijection.py
tests/test_run_config_b0.py
tests/test_run_diff_isoform.py
tests/test_run_manifest_e2.py
tests/test_state_encapsulation.py
tests/test_sweep_analysis.py
tests/test_switch_combine_a2.py
tests/test_switch_diff_isoform_agg_scope.py
tests/test_switch_length_degenerate_pairs.py
tests/test_switch_length_strand_and_counts.py
tests/test_switch_pasbed_resolve_b4.py
tests/test_switch_trend_a3.py
tests/test_tfidf_sparse_identity.py
tests/test_trend_metrics.py
tests/test_version_sync.py
tests/test_viz_registry.py
tests/test_viz_strategies_smoke.py
tests/test_viz_tier2_smoke.py
tests/test_viz_tier3_smoke.py
tests/test_viz_tier4_smoke.py
tests/test_wizard_e2e.py
tests/test_yaml_loader.py