.coveragerc
.gitignore
.gitmodules
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.readthedocs.yml
AUTHORS.md
CHANGELOG.md
CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
tox.ini
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.github/workflows/pypi-test.yml
docs/Makefile
docs/authors.md
docs/changelog.md
docs/conf.py
docs/contributing.md
docs/index.md
docs/license.md
docs/readme.md
docs/requirements.txt
docs/_static/.gitignore
scripts/dryrun.py
src/scranpy/__init__.py
src/scranpy/_cpphelpers.py
src/scranpy/_utils.py
src/scranpy.egg-info/PKG-INFO
src/scranpy.egg-info/SOURCES.txt
src/scranpy.egg-info/dependency_links.txt
src/scranpy.egg-info/not-zip-safe
src/scranpy.egg-info/requires.txt
src/scranpy.egg-info/top_level.txt
src/scranpy/aggregation/__init__.py
src/scranpy/aggregation/aggregate_across_cells.py
src/scranpy/aggregation/downsample_by_neighbors.py
src/scranpy/analyze/AnalyzeOptions.py
src/scranpy/analyze/AnalyzeResults.py
src/scranpy/analyze/__init__.py
src/scranpy/analyze/analyze.py
src/scranpy/analyze/dry_analyze.py
src/scranpy/analyze/live_analyze.py
src/scranpy/analyze/run_neighbor_suite.py
src/scranpy/analyze/update.py
src/scranpy/batch_correction/__init__.py
src/scranpy/batch_correction/mnn_correct.py
src/scranpy/clustering/__init__.py
src/scranpy/clustering/build_snn_graph.py
src/scranpy/dimensionality_reduction/__init__.py
src/scranpy/dimensionality_reduction/combine_embeddings.py
src/scranpy/dimensionality_reduction/run_pca.py
src/scranpy/dimensionality_reduction/run_tsne.py
src/scranpy/dimensionality_reduction/run_umap.py
src/scranpy/feature_selection/__init__.py
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src/scranpy/feature_selection/model_gene_variances.py
src/scranpy/feature_set_enrichment/__init__.py
src/scranpy/feature_set_enrichment/hypergeometric_test.py
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src/scranpy/lib/aggregate_across_cells.cpp
src/scranpy/lib/bindings.cpp
src/scranpy/lib/build_snn_graph.cpp
src/scranpy/lib/center_size_factors.cpp
src/scranpy/lib/choose_hvgs.cpp
src/scranpy/lib/downsample_by_neighbors.cpp
src/scranpy/lib/filter_cells.cpp
src/scranpy/lib/find_nearest_neighbors.cpp
src/scranpy/lib/grouped_size_factors.cpp
src/scranpy/lib/hypergeometric_test.cpp
src/scranpy/lib/log_norm_counts.cpp
src/scranpy/lib/mnn_correct.cpp
src/scranpy/lib/model_gene_variances.cpp
src/scranpy/lib/parallel.h
src/scranpy/lib/per_cell_adt_qc_metrics.cpp
src/scranpy/lib/per_cell_crispr_qc_metrics.cpp
src/scranpy/lib/per_cell_rna_qc_metrics.cpp
src/scranpy/lib/run_pca.cpp
src/scranpy/lib/run_tsne.cpp
src/scranpy/lib/run_umap.cpp
src/scranpy/lib/scale_by_neighbors.cpp
src/scranpy/lib/score_feature_set.cpp
src/scranpy/lib/score_markers.cpp
src/scranpy/lib/suggest_adt_qc_filters.cpp
src/scranpy/lib/suggest_crispr_qc_filters.cpp
src/scranpy/lib/suggest_rna_qc_filters.cpp
src/scranpy/marker_detection/__init__.py
src/scranpy/marker_detection/score_markers.py
src/scranpy/nearest_neighbors/__init__.py
src/scranpy/nearest_neighbors/build_neighbor_index.py
src/scranpy/nearest_neighbors/find_nearest_neighbors.py
src/scranpy/normalization/__init__.py
src/scranpy/normalization/center_size_factors.py
src/scranpy/normalization/grouped_size_factors.py
src/scranpy/normalization/log_norm_counts.py
src/scranpy/quality_control/__init__.py
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src/scranpy/quality_control/create_adt_qc_filter.py
src/scranpy/quality_control/create_crispr_qc_filter.py
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src/scranpy/quality_control/guess_mito_from_symbols.py
src/scranpy/quality_control/per_cell_adt_qc_metrics.py
src/scranpy/quality_control/per_cell_crispr_qc_metrics.py
src/scranpy/quality_control/per_cell_rna_qc_metrics.py
src/scranpy/quality_control/suggest_adt_qc_filters.py
src/scranpy/quality_control/suggest_crispr_qc_filters.py
src/scranpy/quality_control/suggest_rna_qc_filters.py
tests/conftest.py
tests/test_aggregate_across_cells.py
tests/test_analyze.py
tests/test_center_size_factors.py
tests/test_choose_hvgs.py
tests/test_combine_embeddings.py
tests/test_create_adt_qc_filter.py
tests/test_create_crispr_qc_filter.py
tests/test_create_rna_qc_filter.py
tests/test_dimreds.py
tests/test_downsample_by_neighbors.py
tests/test_filter_cells.py
tests/test_grouped_size_factors.py
tests/test_guess_mito_from_symbols.py
tests/test_hypergeometric_test.py
tests/test_log_norm_counts.py
tests/test_mnn_correct.py
tests/test_model_gene_variances.py
tests/test_nearest_neighbors.py
tests/test_pca.py
tests/test_per_cell_adt_qc_metrics.py
tests/test_per_cell_crispr_qc_metrics.py
tests/test_per_cell_rna_qc_metrics.py
tests/test_score_feature_set.py
tests/test_score_markers.py
tests/test_snn_graph.py
tests/test_suggest_adt_qc_filters.py
tests/test_suggest_crispr_qc_filters.py
tests/test_suggest_rna_qc_filters.py
tests/data/mock_data.py