.coveragerc
.gitignore
.isort.cfg
.pre-commit-config.yaml
.readthedocs.yml
AUTHORS.md
CHANGELOG.md
CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
tox.ini
.github/workflows/pypi-test.yml
extern/fetch.sh
src/assorthead/__init__.py
src/assorthead/includes.py
src/assorthead.egg-info/PKG-INFO
src/assorthead.egg-info/SOURCES.txt
src/assorthead.egg-info/dependency_links.txt
src/assorthead.egg-info/not-zip-safe
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src/assorthead/include/Eigen/src/plugins/CommonCwiseBinaryOps.h
src/assorthead/include/Eigen/src/plugins/CommonCwiseUnaryOps.h
src/assorthead/include/Eigen/src/plugins/IndexedViewMethods.h
src/assorthead/include/Eigen/src/plugins/MatrixCwiseBinaryOps.h
src/assorthead/include/Eigen/src/plugins/MatrixCwiseUnaryOps.h
src/assorthead/include/Eigen/src/plugins/ReshapedMethods.h
src/assorthead/include/WeightedLowess/WeightedLowess.hpp
src/assorthead/include/aarand/aarand.hpp
src/assorthead/include/annoy/annoylib.h
src/assorthead/include/annoy/kissrandom.h
src/assorthead/include/annoy/mman.h
src/assorthead/include/byteme/ChunkedBufferReader.hpp
src/assorthead/include/byteme/GzipFileReader.hpp
src/assorthead/include/byteme/GzipFileWriter.hpp
src/assorthead/include/byteme/IstreamReader.hpp
src/assorthead/include/byteme/OstreamWriter.hpp
src/assorthead/include/byteme/PerByte.hpp
src/assorthead/include/byteme/RawBufferReader.hpp
src/assorthead/include/byteme/RawBufferWriter.hpp
src/assorthead/include/byteme/RawFileReader.hpp
src/assorthead/include/byteme/RawFileWriter.hpp
src/assorthead/include/byteme/Reader.hpp
src/assorthead/include/byteme/SelfClosingFILE.hpp
src/assorthead/include/byteme/SelfClosingGzFile.hpp
src/assorthead/include/byteme/SomeBufferReader.hpp
src/assorthead/include/byteme/SomeFileReader.hpp
src/assorthead/include/byteme/Writer.hpp
src/assorthead/include/byteme/ZlibBufferReader.hpp
src/assorthead/include/byteme/ZlibBufferWriter.hpp
src/assorthead/include/byteme/byteme.hpp
src/assorthead/include/byteme/magic_numbers.hpp
src/assorthead/include/byteme/temp_file_path.hpp
src/assorthead/include/hnswlib/bruteforce.h
src/assorthead/include/hnswlib/hnswalg.h
src/assorthead/include/hnswlib/hnswlib.h
src/assorthead/include/hnswlib/space_ip.h
src/assorthead/include/hnswlib/space_l2.h
src/assorthead/include/hnswlib/visited_list_pool.h
src/assorthead/include/irlba/irlba.hpp
src/assorthead/include/irlba/lanczos.hpp
src/assorthead/include/irlba/parallel.hpp
src/assorthead/include/irlba/utils.hpp
src/assorthead/include/irlba/wrappers.hpp
src/assorthead/include/kmeans/Base.hpp
src/assorthead/include/kmeans/Details.hpp
src/assorthead/include/kmeans/HartiganWong.hpp
src/assorthead/include/kmeans/InitializeKmeansPP.hpp
src/assorthead/include/kmeans/InitializeNone.hpp
src/assorthead/include/kmeans/InitializePCAPartition.hpp
src/assorthead/include/kmeans/InitializeRandom.hpp
src/assorthead/include/kmeans/Kmeans.hpp
src/assorthead/include/kmeans/Lloyd.hpp
src/assorthead/include/kmeans/MiniBatch.hpp
src/assorthead/include/kmeans/QuickSearch.hpp
src/assorthead/include/kmeans/compute_centroids.hpp
src/assorthead/include/kmeans/compute_wcss.hpp
src/assorthead/include/kmeans/is_edge_case.hpp
src/assorthead/include/kmeans/random.hpp
src/assorthead/include/knncolle/knncolle.hpp
src/assorthead/include/knncolle/Annoy/Annoy.hpp
src/assorthead/include/knncolle/BruteForce/BruteForce.hpp
src/assorthead/include/knncolle/Hnsw/Hnsw.hpp
src/assorthead/include/knncolle/Kmknn/Kmknn.hpp
src/assorthead/include/knncolle/VpTree/VpTree.hpp
src/assorthead/include/knncolle/utils/Base.hpp
src/assorthead/include/knncolle/utils/NeighborQueue.hpp
src/assorthead/include/knncolle/utils/distances.hpp
src/assorthead/include/knncolle/utils/find_nearest_neighbors.hpp
src/assorthead/include/mnncorrect/AutomaticOrder.hpp
src/assorthead/include/mnncorrect/CustomOrder.hpp
src/assorthead/include/mnncorrect/MnnCorrect.hpp
src/assorthead/include/mnncorrect/ReferencePolicy.hpp
src/assorthead/include/mnncorrect/RobustAverage.hpp
src/assorthead/include/mnncorrect/correct_target.hpp
src/assorthead/include/mnncorrect/find_mutual_nns.hpp
src/assorthead/include/mnncorrect/fuse_nn_results.hpp
src/assorthead/include/mnncorrect/restore_order.hpp
src/assorthead/include/mnncorrect/utils.hpp
src/assorthead/include/powerit/PowerIterations.hpp
src/assorthead/include/qdtsne/gaussian.hpp
src/assorthead/include/qdtsne/interpolate.hpp
src/assorthead/include/qdtsne/qdtsne.hpp
src/assorthead/include/qdtsne/sptree.hpp
src/assorthead/include/qdtsne/symmetrize.hpp
src/assorthead/include/qdtsne/tsne.hpp
src/assorthead/include/qdtsne/utils.hpp
src/assorthead/include/scran/scran.hpp
src/assorthead/include/scran/aggregation/AggregateAcrossCells.hpp
src/assorthead/include/scran/aggregation/DownsampleByNeighbors.hpp
src/assorthead/include/scran/clustering/BuildSnnGraph.hpp
src/assorthead/include/scran/clustering/ClusterSnnGraph.hpp
src/assorthead/include/scran/clustering/igraph_utils.hpp
src/assorthead/include/scran/differential_analysis/MatrixCalculator.hpp
src/assorthead/include/scran/differential_analysis/PairwiseEffects.hpp
src/assorthead/include/scran/differential_analysis/ScoreMarkers.hpp
src/assorthead/include/scran/differential_analysis/SummarizeEffects.hpp
src/assorthead/include/scran/differential_analysis/auc.hpp
src/assorthead/include/scran/differential_analysis/cohens_d.hpp
src/assorthead/include/scran/differential_analysis/simple_diff.hpp
src/assorthead/include/scran/differential_analysis/summarize_comparisons.hpp
src/assorthead/include/scran/dimensionality_reduction/MultiBatchPca.hpp
src/assorthead/include/scran/dimensionality_reduction/ResidualPca.hpp
src/assorthead/include/scran/dimensionality_reduction/ScaleByNeighbors.hpp
src/assorthead/include/scran/dimensionality_reduction/SimplePca.hpp
src/assorthead/include/scran/dimensionality_reduction/blocking.hpp
src/assorthead/include/scran/dimensionality_reduction/convert.hpp
src/assorthead/include/scran/dimensionality_reduction/utils.hpp
src/assorthead/include/scran/dimensionality_reduction/wrappers.hpp
src/assorthead/include/scran/feature_selection/ChooseHvgs.hpp
src/assorthead/include/scran/feature_selection/FitVarianceTrend.hpp
src/assorthead/include/scran/feature_selection/ModelGeneVariances.hpp
src/assorthead/include/scran/feature_selection/blocked_variances.hpp
src/assorthead/include/scran/feature_set_enrichment/HypergeometricTail.hpp
src/assorthead/include/scran/feature_set_enrichment/ScoreFeatureSet.hpp
src/assorthead/include/scran/normalization/CenterSizeFactors.hpp
src/assorthead/include/scran/normalization/ChoosePseudoCount.hpp
src/assorthead/include/scran/normalization/GroupedSizeFactors.hpp
src/assorthead/include/scran/normalization/LogNormCounts.hpp
src/assorthead/include/scran/normalization/MedianSizeFactors.hpp
src/assorthead/include/scran/normalization/SanitizeSizeFactors.hpp
src/assorthead/include/scran/normalization/quick_grouped_size_factors.hpp
src/assorthead/include/scran/quality_control/ChooseOutlierFilters.hpp
src/assorthead/include/scran/quality_control/ComputeMedianMad.hpp
src/assorthead/include/scran/quality_control/FilterCells.hpp
src/assorthead/include/scran/quality_control/PerCellAdtQcMetrics.hpp
src/assorthead/include/scran/quality_control/PerCellCrisprQcMetrics.hpp
src/assorthead/include/scran/quality_control/PerCellQcMetrics.hpp
src/assorthead/include/scran/quality_control/PerCellRnaQcMetrics.hpp
src/assorthead/include/scran/quality_control/SuggestAdtQcFilters.hpp
src/assorthead/include/scran/quality_control/SuggestCrisprQcFilters.hpp
src/assorthead/include/scran/quality_control/SuggestRnaQcFilters.hpp
src/assorthead/include/scran/quality_control/utils.hpp
src/assorthead/include/scran/utils/average_vectors.hpp
src/assorthead/include/scran/utils/blocking.hpp
src/assorthead/include/scran/utils/macros.hpp
src/assorthead/include/scran/utils/subset_vector.hpp
src/assorthead/include/scran/utils/vector_to_pointers.hpp
src/assorthead/include/singlepp/BasicBuilder.hpp
src/assorthead/include/singlepp/BasicScorer.hpp
src/assorthead/include/singlepp/ChooseClassicMarkers.hpp
src/assorthead/include/singlepp/Classifier.hpp
src/assorthead/include/singlepp/IntegratedBuilder.hpp
src/assorthead/include/singlepp/IntegratedScorer.hpp
src/assorthead/include/singlepp/Markers.hpp
src/assorthead/include/singlepp/annotate_cells.hpp
src/assorthead/include/singlepp/build_indices.hpp
src/assorthead/include/singlepp/compute_scores.hpp
src/assorthead/include/singlepp/fine_tune.hpp
src/assorthead/include/singlepp/load_references.hpp
src/assorthead/include/singlepp/macros.hpp
src/assorthead/include/singlepp/process_features.hpp
src/assorthead/include/singlepp/scaled_ranks.hpp
src/assorthead/include/singlepp/singlepp.hpp
src/assorthead/include/tatami/tatami.hpp
src/assorthead/include/tatami/base/Extractor.hpp
src/assorthead/include/tatami/base/Matrix.hpp
src/assorthead/include/tatami/base/Options.hpp
src/assorthead/include/tatami/base/SparseRange.hpp
src/assorthead/include/tatami/base/utils.hpp
src/assorthead/include/tatami/dense/DenseMatrix.hpp
src/assorthead/include/tatami/dense/VirtualDenseMatrix.hpp
src/assorthead/include/tatami/dense/convert_to_dense.hpp
src/assorthead/include/tatami/isometric/arith_utils.hpp
src/assorthead/include/tatami/isometric/boolean_utils.hpp
src/assorthead/include/tatami/isometric/compare_utils.hpp
src/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOp.hpp
src/assorthead/include/tatami/isometric/binary/arith_helpers.hpp
src/assorthead/include/tatami/isometric/binary/boolean_helpers.hpp
src/assorthead/include/tatami/isometric/binary/compare_helpers.hpp
src/assorthead/include/tatami/isometric/binary/utils.hpp
src/assorthead/include/tatami/isometric/unary/DelayedUnaryIsometricOp.hpp
src/assorthead/include/tatami/isometric/unary/arith_helpers.hpp
src/assorthead/include/tatami/isometric/unary/boolean_helpers.hpp
src/assorthead/include/tatami/isometric/unary/compare_helpers.hpp
src/assorthead/include/tatami/isometric/unary/math_helpers.hpp
src/assorthead/include/tatami/other/DelayedBind.hpp
src/assorthead/include/tatami/other/DelayedCast.hpp
src/assorthead/include/tatami/other/DelayedTranspose.hpp
src/assorthead/include/tatami/sparse/CompressedSparseMatrix.hpp
src/assorthead/include/tatami/sparse/FragmentedSparseMatrix.hpp
src/assorthead/include/tatami/sparse/SemiCompressedSparseMatrix.hpp
src/assorthead/include/tatami/sparse/SparseSecondaryExtractorCore.hpp
src/assorthead/include/tatami/sparse/convert_to_compressed_sparse.hpp
src/assorthead/include/tatami/sparse/convert_to_fragmented_sparse.hpp
src/assorthead/include/tatami/sparse/primary_extraction.hpp
src/assorthead/include/tatami/sparse/utils.hpp
src/assorthead/include/tatami/stats/counts.hpp
src/assorthead/include/tatami/stats/grouped_medians.hpp
src/assorthead/include/tatami/stats/grouped_sums.hpp
src/assorthead/include/tatami/stats/medians.hpp
src/assorthead/include/tatami/stats/ranges.hpp
src/assorthead/include/tatami/stats/sums.hpp
src/assorthead/include/tatami/stats/utils.hpp
src/assorthead/include/tatami/stats/variances.hpp
src/assorthead/include/tatami/subset/DelayedSubset.hpp
src/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp
src/assorthead/include/tatami/subset/DelayedSubsetSorted.hpp
src/assorthead/include/tatami/subset/DelayedSubsetSortedUnique.hpp
src/assorthead/include/tatami/subset/DelayedSubsetUnique.hpp
src/assorthead/include/tatami/subset/make_DelayedSubset.hpp
src/assorthead/include/tatami/subset/utils.hpp
src/assorthead/include/tatami/utils/ArrayView.hpp
src/assorthead/include/tatami/utils/ElementType.hpp
src/assorthead/include/tatami/utils/Oracles.hpp
src/assorthead/include/tatami/utils/SomeNumericArray.hpp
src/assorthead/include/tatami/utils/bind_intersection.hpp
src/assorthead/include/tatami/utils/compress_sparse_triplets.hpp
src/assorthead/include/tatami/utils/convert_to_dense.hpp
src/assorthead/include/tatami/utils/convert_to_sparse.hpp
src/assorthead/include/tatami/utils/process_consecutive_indices.hpp
src/assorthead/include/tatami/utils/wrap_shared_ptr.hpp
src/assorthead/include/umappp/NeighborList.hpp
src/assorthead/include/umappp/Umap.hpp
src/assorthead/include/umappp/combine_neighbor_sets.hpp
src/assorthead/include/umappp/find_ab.hpp
src/assorthead/include/umappp/neighbor_similarities.hpp
src/assorthead/include/umappp/optimize_layout.hpp
src/assorthead/include/umappp/spectral_init.hpp
src/assorthead/include/umappp/umappp.hpp
tests/conftest.py
tests/test_includes.py