GUIDE.md
LABEL_QUALITY_VARIANTS.md
LICENSE
MANIFEST.in
PUBLISHING.md
README.md
pyproject.toml
uv.lock
scintilla/__init__.py
scintilla/__main__.py
scintilla/analysis_config.py
scintilla/config.py
scintilla/annotation/__init__.py
scintilla/annotation/label_transfer.py
scintilla/annotation/marker_based.py
scintilla/annotation/over_representation.py
scintilla/annotation/rank_genes.py
scintilla/batch_correction/__init__.py
scintilla/batch_correction/bbknn.py
scintilla/batch_correction/benchmark.py
scintilla/batch_correction/combat.py
scintilla/batch_correction/harmony.py
scintilla/batch_correction/metrics.py
scintilla/batch_correction/scanorama.py
scintilla/benchmarking/__init__.py
scintilla/benchmarking/comparison.py
scintilla/benchmarking/profiler.py
scintilla/benchmarking/reporter.py
scintilla/benchmarking/reproducibility.py
scintilla/benchmarking/scalability.py
scintilla/benchmarking/time_estimator.py
scintilla/classification/__init__.py
scintilla/classification/benchmark.py
scintilla/classification/diagnostics.py
scintilla/classification/feature_importance.py
scintilla/classification/label_quality_variants.py
scintilla/classification/models.py
scintilla/classification/run.py
scintilla/classification/visualise.py
scintilla/cli/__init__.py
scintilla/cli/main.py
scintilla/cli/commands/__init__.py
scintilla/cli/commands/annotate.py
scintilla/cli/commands/batch_correct.py
scintilla/cli/commands/benchmark_all.py
scintilla/cli/commands/classify.py
scintilla/cli/commands/cluster.py
scintilla/cli/commands/de.py
scintilla/cli/commands/eda.py
scintilla/cli/commands/estimate_time.py
scintilla/cli/commands/feature_select.py
scintilla/cli/commands/generate_config.py
scintilla/cli/commands/label_quality.py
scintilla/cli/commands/normalise.py
scintilla/cli/commands/preprocess.py
scintilla/cli/commands/reduce.py
scintilla/cli/commands/run_all.py
scintilla/clustering/__init__.py
scintilla/clustering/benchmark.py
scintilla/clustering/consensus.py
scintilla/clustering/dbscan.py
scintilla/clustering/hdbscan.py
scintilla/clustering/hierarchical.py
scintilla/clustering/kmeans.py
scintilla/clustering/leiden.py
scintilla/clustering/louvain.py
scintilla/clustering/run.py
scintilla/clustering/similarity_assembly.py
scintilla/clustering/spectral.py
scintilla/clustering/utils.py
scintilla/differential_expression/__init__.py
scintilla/differential_expression/benchmark.py
scintilla/differential_expression/permutation.py
scintilla/differential_expression/pseudobulk.py
scintilla/differential_expression/rank_genes.py
scintilla/differential_expression/ttest.py
scintilla/differential_expression/utils.py
scintilla/differential_expression/wilcoxon.py
scintilla/dimensionality_reduction/__init__.py
scintilla/dimensionality_reduction/benchmark.py
scintilla/dimensionality_reduction/diffusion_map.py
scintilla/dimensionality_reduction/force_directed.py
scintilla/dimensionality_reduction/tsne.py
scintilla/dimensionality_reduction/umap.py
scintilla/eda/__init__.py
scintilla/eda/summary.py
scintilla/evaluation/__init__.py
scintilla/evaluation/batch_metrics.py
scintilla/evaluation/classification_metrics.py
scintilla/evaluation/clustering_metrics.py
scintilla/evaluation/embedding_metrics.py
scintilla/evaluation/patient_level.py
scintilla/feature_selection/__init__.py
scintilla/feature_selection/benchmark.py
scintilla/feature_selection/boruta.py
scintilla/feature_selection/hvg.py
scintilla/feature_selection/mrmr.py
scintilla/feature_selection/mutual_information.py
scintilla/feature_selection/pca_loadings.py
scintilla/io/__init__.py
scintilla/io/exporters.py
scintilla/io/loaders.py
scintilla/preprocessing/__init__.py
scintilla/preprocessing/aggregation.py
scintilla/preprocessing/benchmark.py
scintilla/preprocessing/normality.py
scintilla/preprocessing/pca.py
scintilla/preprocessing/transformations.py
scintilla/statistical_tests/__init__.py
scintilla/statistical_tests/adaptive.py
scintilla/statistical_tests/anova.py
scintilla/statistical_tests/bootstrap.py
scintilla/statistical_tests/boxm.py
scintilla/statistical_tests/correction.py
scintilla/statistical_tests/dunns.py
scintilla/statistical_tests/effect_sizes.py
scintilla/statistical_tests/kruskal.py
scintilla/statistical_tests/permutation.py
scintilla/statistical_tests/rank_aggregation.py
scintilla/visualisation/__init__.py
scintilla/visualisation/batch_plots.py
scintilla/visualisation/benchmark_summary.py
scintilla/visualisation/classification_plots.py
scintilla/visualisation/clustering_plots.py
scintilla/visualisation/de_plots.py
scintilla/visualisation/embedding_plots.py
scintilla/visualisation/gene_plots.py
scintilla/visualisation/pca_plots.py
scintilla/visualisation/sankey_plots.py
scintilla/visualisation/transformation_plots.py
scintilla_py.egg-info/PKG-INFO
scintilla_py.egg-info/SOURCES.txt
scintilla_py.egg-info/dependency_links.txt
scintilla_py.egg-info/entry_points.txt
scintilla_py.egg-info/requires.txt
scintilla_py.egg-info/top_level.txt
tests/test_analysis_config_seeding.py
tests/test_cell_type_defaults.py
tests/test_de_benchmark.py
tests/test_followup_fixes.py
tests/test_fragmentation.py
tests/test_label_quality_reruns.py
tests/test_label_quality_variants.py
tests/test_label_transfer.py
tests/test_matplotlib_isolation.py
tests/test_normality_visibility.py
tests/test_rank_genes_groups.py
tests/test_visible_benchmark_failures.py