.gitignore
.readthedocs.yaml
CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
SECURITY.md
pyproject.toml
.github/workflows/publish.yml
.github/workflows/tests.yml
docs/changelog.md
docs/conf.py
docs/faq.md
docs/index.md
docs/installation.md
docs/license.md
docs/quickstart.md
docs/requirements.txt
docs/_static/css/custom.css
docs/api/index.md
docs/tutorials/index.md
docs/tutorials/pbmc10k_hvg_compare.ipynb
docs/user_guide/index.md
docs/user_guide/method.md
docs/user_guide/outputs.md
docs/user_guide/parameters.md
examples/ablation_scale_logfc.py
examples/adt14_res_sweep.py
examples/adt_auto_k_protein_gold.py
examples/adt_crossval_shadowed.py
examples/adt_gold_benchmark.py
examples/adt_multi_validation.py
examples/adt_neighbor_contrast.py
examples/adt_resolution_check.py
examples/adt_tuning_sweep.py
examples/alpha_panel.py
examples/alpha_panel_cap_probe.py
examples/auto_n_benchmark.py
examples/auto_n_holdout_eval.py
examples/auto_n_k_inventory.py
examples/auto_n_populations.py
examples/auto_n_separability_probe.py
examples/auto_n_structure_solve.py
examples/auto_n_v2_benchmark.py
examples/auto_n_vote_spread.py
examples/blend_global_deprivation.py
examples/build_gold_panel_extra.py
examples/cap_allocation_validate.py
examples/cap_merge_threshold_calibration.py
examples/cap_merge_threshold_sweep_real.py
examples/cap_merge_validate.py
examples/cellbrf_style_benchmark.py
examples/cluster_pool_analysis.py
examples/cluster_pool_extend.py
examples/cluster_pool_panel.py
examples/cluster_pool_table.py
examples/coverage_allocation_panel.py
examples/crafted_recall_panel.py
examples/deficit_probe.py
examples/deprivation_topup.py
examples/duo_res_sweep.py
examples/final_comparison.py
examples/fine_gene_budget_probe.py
examples/fine_res_and_shortk_probe.py
examples/gold15_auto_k_exact_eval.py
examples/gold15_ksweep_missing.py
examples/gold_expansion_probe.py
examples/hard_task_benchmark.py
examples/hvg_baselines.py
examples/iterate_rounds.py
examples/l1_k_budget_panel.py
examples/merge_tolerant_metric.py
examples/mixhvg_comparison.py
examples/p1_multi_dataset_benchmark.py
examples/p2_benchmark.py
examples/p3_public_validation.py
examples/paper_extra_metrics.py
examples/pbmc3k_benchmark.py
examples/pool_comparison.py
examples/quota_allocation.py
examples/run_alpha_panel.sh
examples/run_followups.sh
examples/signal_hunt.py
examples/sorted_gold_panel.py
examples/split_support_probe.py
examples/structure_vs_scanpy_probe.py
examples/umap3d_bestk_probe.py
examples/umap3d_cores.py
examples/umap3d_knn_density.py
examples/umap3d_sensitivity.py
examples/umap3d_smoke.py
examples/unit_boundary_probe.py
examples/unit_spec_panel.py
examples/v4_alpha_sweep.py
examples/v4_consensus_alpha.py
examples/v4_deficit_dissect.py
examples/zheng_k_sweep_probe.py
src/scfair/__init__.py
src/scfair/_utils.py
src/scfair/_version.py
src/scfair/py.typed
src/scfair/pp/__init__.py
src/scfair/pp/_auto_n.py
src/scfair/pp/_diagnosis.py
src/scfair/pp/_granularity.py
src/scfair/pp/_highly_variable_genes.py
src/scfair/pp/_options.py
src/scfair/pp/_raw_counts.py
tests/conftest.py
tests/test_auto_n.py
tests/test_diagnosis.py
tests/test_granularity.py
tests/test_highly_variable_genes.py
tests/test_rare_marker_recovery.py
tests/test_raw_counts.py