.coveragerc
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AUTHORS.md
CHANGELOG.md
CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
README.md
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setup.py
tox.ini
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docs/Makefile
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docs/conf.py
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docs/requirements.txt
docs/_static/.gitignore
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extern/libscran/LICENSE
extern/libscran/README.md
extern/libscran/.github/workflows/doxygenate.yaml
extern/libscran/.github/workflows/run-tests.yaml
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extern/libscran/extern/CMakeLists.txt
extern/libscran/gallery/CMakeLists.txt
extern/libscran/gallery/minimal.cpp
extern/libscran/gallery/pca_test.cpp
extern/libscran/include/scran/scran.hpp
extern/libscran/include/scran/aggregation/AggregateAcrossCells.hpp
extern/libscran/include/scran/aggregation/DownsampleByNeighbors.hpp
extern/libscran/include/scran/clustering/BuildSnnGraph.hpp
extern/libscran/include/scran/clustering/ClusterSnnGraph.hpp
extern/libscran/include/scran/clustering/igraph_utils.hpp
extern/libscran/include/scran/differential_analysis/MatrixCalculator.hpp
extern/libscran/include/scran/differential_analysis/PairwiseEffects.hpp
extern/libscran/include/scran/differential_analysis/ScoreMarkers.hpp
extern/libscran/include/scran/differential_analysis/SummarizeEffects.hpp
extern/libscran/include/scran/differential_analysis/auc.hpp
extern/libscran/include/scran/differential_analysis/cohens_d.hpp
extern/libscran/include/scran/differential_analysis/simple_diff.hpp
extern/libscran/include/scran/differential_analysis/summarize_comparisons.hpp
extern/libscran/include/scran/dimensionality_reduction/MultiBatchPca.hpp
extern/libscran/include/scran/dimensionality_reduction/ResidualPca.hpp
extern/libscran/include/scran/dimensionality_reduction/ScaleByNeighbors.hpp
extern/libscran/include/scran/dimensionality_reduction/SimplePca.hpp
extern/libscran/include/scran/dimensionality_reduction/blocking.hpp
extern/libscran/include/scran/dimensionality_reduction/convert.hpp
extern/libscran/include/scran/dimensionality_reduction/utils.hpp
extern/libscran/include/scran/dimensionality_reduction/wrappers.hpp
extern/libscran/include/scran/feature_selection/ChooseHvgs.hpp
extern/libscran/include/scran/feature_selection/FitVarianceTrend.hpp
extern/libscran/include/scran/feature_selection/ModelGeneVariances.hpp
extern/libscran/include/scran/feature_selection/blocked_variances.hpp
extern/libscran/include/scran/feature_set_enrichment/HypergeometricTail.hpp
extern/libscran/include/scran/feature_set_enrichment/ScoreFeatureSet.hpp
extern/libscran/include/scran/normalization/CenterSizeFactors.hpp
extern/libscran/include/scran/normalization/ChoosePseudoCount.hpp
extern/libscran/include/scran/normalization/GroupedSizeFactors.hpp
extern/libscran/include/scran/normalization/LogNormCounts.hpp
extern/libscran/include/scran/normalization/MedianSizeFactors.hpp
extern/libscran/include/scran/normalization/utils.hpp
extern/libscran/include/scran/quality_control/ChooseOutlierFilters.hpp
extern/libscran/include/scran/quality_control/ComputeMedianMad.hpp
extern/libscran/include/scran/quality_control/FilterCells.hpp
extern/libscran/include/scran/quality_control/PerCellAdtQcMetrics.hpp
extern/libscran/include/scran/quality_control/PerCellCrisprQcMetrics.hpp
extern/libscran/include/scran/quality_control/PerCellQcMetrics.hpp
extern/libscran/include/scran/quality_control/PerCellRnaQcMetrics.hpp
extern/libscran/include/scran/quality_control/SuggestAdtQcFilters.hpp
extern/libscran/include/scran/quality_control/SuggestCrisprQcFilters.hpp
extern/libscran/include/scran/quality_control/SuggestRnaQcFilters.hpp
extern/libscran/include/scran/quality_control/utils.hpp
extern/libscran/include/scran/utils/average_vectors.hpp
extern/libscran/include/scran/utils/blocking.hpp
extern/libscran/include/scran/utils/macros.hpp
extern/libscran/include/scran/utils/subset_vector.hpp
extern/libscran/include/scran/utils/vector_to_pointers.hpp
extern/libscran/tests/CMakeLists.txt
extern/libscran/tests/README.md
extern/libscran/tests/src/aggregation/AggregateAcrossCells.cpp
extern/libscran/tests/src/aggregation/DownsampleByNeighbors.cpp
extern/libscran/tests/src/clustering/BuildSnnGraph.cpp
extern/libscran/tests/src/clustering/ClusterSnnGraph.cpp
extern/libscran/tests/src/data/Simulator.hpp
extern/libscran/tests/src/data/data.h
extern/libscran/tests/src/data/data_sparse.cpp
extern/libscran/tests/src/differential_analysis/MatrixCalculator.cpp
extern/libscran/tests/src/differential_analysis/PairwiseEffects.cpp
extern/libscran/tests/src/differential_analysis/ScoreMarkers.cpp
extern/libscran/tests/src/differential_analysis/auc.cpp
extern/libscran/tests/src/differential_analysis/cohens_d.cpp
extern/libscran/tests/src/differential_analysis/simple_diff.cpp
extern/libscran/tests/src/differential_analysis/summarize_comparisons.cpp
extern/libscran/tests/src/differential_analysis/utils.h
extern/libscran/tests/src/dimensionality_reduction/MultiBatchPca.cpp
extern/libscran/tests/src/dimensionality_reduction/ResidualPca.cpp
extern/libscran/tests/src/dimensionality_reduction/ScaleByNeighbors.cpp
extern/libscran/tests/src/dimensionality_reduction/SimplePca.cpp
extern/libscran/tests/src/dimensionality_reduction/compare_pcs.h
extern/libscran/tests/src/dimensionality_reduction/convert.cpp
extern/libscran/tests/src/dimensionality_reduction/utils.cpp
extern/libscran/tests/src/feature_selection/ChooseHvgs.cpp
extern/libscran/tests/src/feature_selection/FitVarianceTrend.cpp
extern/libscran/tests/src/feature_selection/ModelGeneVariances.cpp
extern/libscran/tests/src/feature_set_enrichment/HypergeometricTail.cpp
extern/libscran/tests/src/feature_set_enrichment/ScoreFeatureSet.cpp
extern/libscran/tests/src/normalization/CenterSizeFactors.cpp
extern/libscran/tests/src/normalization/ChoosePseudoCount.cpp
extern/libscran/tests/src/normalization/GroupedSizeFactors.cpp
extern/libscran/tests/src/normalization/LogNormCounts.cpp
extern/libscran/tests/src/normalization/MedianSizeFactors.cpp
extern/libscran/tests/src/quality_control/ChooseOutlierFilters.cpp
extern/libscran/tests/src/quality_control/ComputeMedianMad.cpp
extern/libscran/tests/src/quality_control/FilterCells.cpp
extern/libscran/tests/src/quality_control/PerCellAdtQcMetrics.cpp
extern/libscran/tests/src/quality_control/PerCellCrisprQcMetrics.cpp
extern/libscran/tests/src/quality_control/PerCellQcMetrics.cpp
extern/libscran/tests/src/quality_control/PerCellRnaQcMetrics.cpp
extern/libscran/tests/src/quality_control/SuggestAdtQcFilters.cpp
extern/libscran/tests/src/quality_control/SuggestCrisprQcFilters.cpp
extern/libscran/tests/src/quality_control/SuggestRnaQcFilters.cpp
extern/libscran/tests/src/quality_control/utils.h
extern/libscran/tests/src/utils/average_vectors.cpp
extern/libscran/tests/src/utils/blocking.cpp
extern/libscran/tests/src/utils/compare_almost_equal.h
extern/libscran/tests/src/utils/compare_vectors.h
extern/libscran/tests/src/utils/custom_parallel.h
extern/libscran/tests/src/utils/macros.h
extern/libscran/tests/src/utils/subset_vector.cpp
extern/weightedlowess/.git
extern/weightedlowess/CMakeLists.txt
extern/weightedlowess/LICENSE
extern/weightedlowess/README.md
extern/weightedlowess/.github/workflows/compare-limma.yaml
extern/weightedlowess/.github/workflows/doxygenate.yaml
extern/weightedlowess/.github/workflows/run-tests.yaml
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extern/weightedlowess/include/WeightedLowess/WeightedLowess.hpp
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extern/weightedlowess/tests/src/basic.cpp
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extern/weightedlowess/tests/src/runners.cpp
extern/weightedlowess/tests/src/ties.cpp
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src/scranpy/__init__.py
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src/scranpy.egg-info/requires.txt
src/scranpy.egg-info/top_level.txt
src/scranpy/feature_selection/__init__.py
src/scranpy/feature_selection/model_gene_variances.py
src/scranpy/lib/log_norm_counts.cpp
src/scranpy/lib/model_gene_variances.cpp
src/scranpy/lib/per_cell_rna_qc_metrics.cpp
src/scranpy/lib/suggest_rna_qc_filters.cpp
src/scranpy/normalization/__init__.py
src/scranpy/normalization/log_norm_counts.py
src/scranpy/quality_control/__init__.py
src/scranpy/quality_control/rna.py
tests/conftest.py
tests/test_log_norm_counts.py
tests/test_model_gene_variances.py
tests/test_quality_control_steps.py