LICENSE
README.md
pyproject.toml
tcrsift/__init__.py
tcrsift/_dtypes.py
tcrsift/_regen_canonical_constants.py
tcrsift/annotate.py
tcrsift/annotate_tcrs.py
tcrsift/assemble.py
tcrsift/attribution.py
tcrsift/candidate.py
tcrsift/cli.py
tcrsift/clonotype.py
tcrsift/cohort.py
tcrsift/config.py
tcrsift/data.py
tcrsift/datacache.py
tcrsift/filter.py
tcrsift/format.py
tcrsift/genes.py
tcrsift/gex.py
tcrsift/insilico_filter.py
tcrsift/leaders.py
tcrsift/loader.py
tcrsift/mnemonic.py
tcrsift/model.py
tcrsift/pgen.py
tcrsift/pgen_models.py
tcrsift/phenotype.py
tcrsift/plots.py
tcrsift/provenance.py
tcrsift/qc.py
tcrsift/qc_battery.py
tcrsift/report.py
tcrsift/sample_sheet.py
tcrsift/sct.py
tcrsift/selection.py
tcrsift/seqprob.py
tcrsift/signature_methods.py
tcrsift/signatures.py
tcrsift/sigpep.py
tcrsift/sort_qc.py
tcrsift/til.py
tcrsift/til_select.py
tcrsift/unify.py
tcrsift/validation.py
tcrsift/version.py
tcrsift/vregion.py
tcrsift.egg-info/PKG-INFO
tcrsift.egg-info/SOURCES.txt
tcrsift.egg-info/dependency_links.txt
tcrsift.egg-info/entry_points.txt
tcrsift.egg-info/requires.txt
tcrsift.egg-info/top_level.txt
tcrsift/refseqs/PROVENANCE.md
tcrsift/refseqs/__init__.py
tcrsift/refseqs/canonical_constants.fasta
tcrsift/refseqs/canonical_constants_alleles.fasta
tcrsift/refseqs/kmer_pgen_alpha.npz
tcrsift/refseqs/kmer_pgen_beta.npz
tcrsift/refseqs/kmer_ppost_alpha.npz
tcrsift/refseqs/kmer_ppost_beta.npz
tcrsift/refseqs/observed_pbmc_10x.csv.gz
tcrsift/refseqs/vgene_leaders.csv.gz
tests/test_allele_reasons_and_audit.py
tests/test_annotate.py
tests/test_annotate_confidence.py
tests/test_annotate_fuzzy.py
tests/test_annotate_metadata.py
tests/test_annotate_tcrs.py
tests/test_assemble.py
tests/test_assemble_alleles.py
tests/test_assemble_codon_optimization.py
tests/test_assemble_constants.py
tests/test_assemble_qc_extended.py
tests/test_assemble_validate_strict.py
tests/test_attribution.py
tests/test_candidate.py
tests/test_cells_per_sample_stacked.py
tests/test_chosen_helpers.py
tests/test_cli.py
tests/test_cli_config_contigs.py
tests/test_clone_method_long.py
tests/test_clonotype.py
tests/test_clonotype_denominator_fix.py
tests/test_cohort.py
tests/test_config.py
tests/test_cross_donor_venn.py
tests/test_data.py
tests/test_datacache.py
tests/test_dtypes.py
tests/test_dual_alpha_real_contigs.py
tests/test_e2e.py
tests/test_expansion_qc.py
tests/test_filter.py
tests/test_finish_select_report.py
tests/test_format.py
tests/test_freq_prism_grid.py
tests/test_funnel_extensions.py
tests/test_genes.py
tests/test_germline_leaders.py
tests/test_gex.py
tests/test_insilico_filter.py
tests/test_leader_kozak_qc.py
tests/test_load_contigs.py
tests/test_loader.py
tests/test_mnemonic.py
tests/test_model.py
tests/test_no_assemble.py
tests/test_package.py
tests/test_pgen.py
tests/test_pgen_models_no_olga.py
tests/test_pgen_plots.py
tests/test_phenotype.py
tests/test_plots_43_remaining.py
tests/test_plots_annotation.py
tests/test_plots_freq_prism_scatter.py
tests/test_plots_pretty_labels.py
tests/test_plots_prism_components.py
tests/test_plots_rank_family.py
tests/test_plots_tcr_pdf_columns.py
tests/test_plots_vgene_usage.py
tests/test_ppost_provenance.py
tests/test_prism_per_condition.py
tests/test_prism_route.py
tests/test_provenance.py
tests/test_qc.py
tests/test_qc_battery.py
tests/test_qc_warnings_schema.py
tests/test_report_bundle.py
tests/test_run_sheet_contigs.py
tests/test_sample_sheet.py
tests/test_sanity_fixes.py
tests/test_sct.py
tests/test_select_command.py
tests/test_selected_report.py
tests/test_selection.py
tests/test_seqprob.py
tests/test_set_overlap.py
tests/test_signature_methods.py
tests/test_signature_picks_per_method.py
tests/test_signature_scores.py
tests/test_signatures.py
tests/test_sort_qc.py
tests/test_specificity_and_output.py
tests/test_synthesis_qc.py
tests/test_tier_helpers.py
tests/test_til.py
tests/test_til_select.py
tests/test_unify.py
tests/test_vregion.py