.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.py
extern/manifest.csv
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/Options.hpp
src/assorthead/include/WeightedLowess/SortBy.hpp
src/assorthead/include/WeightedLowess/WeightedLowess.hpp
src/assorthead/include/WeightedLowess/compute.hpp
src/assorthead/include/WeightedLowess/fit.hpp
src/assorthead/include/WeightedLowess/parallelize.hpp
src/assorthead/include/WeightedLowess/robust.hpp
src/assorthead/include/WeightedLowess/window.hpp
src/assorthead/include/aarand/aarand.hpp
src/assorthead/include/annoy/annoygomodule.h
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/chihaya/binary_arithmetic.hpp
src/assorthead/include/chihaya/binary_comparison.hpp
src/assorthead/include/chihaya/binary_logic.hpp
src/assorthead/include/chihaya/chihaya.hpp
src/assorthead/include/chihaya/combine.hpp
src/assorthead/include/chihaya/constant_array.hpp
src/assorthead/include/chihaya/custom_array.hpp
src/assorthead/include/chihaya/dense_array.hpp
src/assorthead/include/chihaya/dimnames.hpp
src/assorthead/include/chihaya/external_hdf5.hpp
src/assorthead/include/chihaya/matrix_product.hpp
src/assorthead/include/chihaya/minimal_array.hpp
src/assorthead/include/chihaya/sparse_matrix.hpp
src/assorthead/include/chihaya/subset.hpp
src/assorthead/include/chihaya/subset_assignment.hpp
src/assorthead/include/chihaya/transpose.hpp
src/assorthead/include/chihaya/unary_arithmetic.hpp
src/assorthead/include/chihaya/unary_comparison.hpp
src/assorthead/include/chihaya/unary_logic.hpp
src/assorthead/include/chihaya/unary_math.hpp
src/assorthead/include/chihaya/unary_special_check.hpp
src/assorthead/include/chihaya/utils_arithmetic.hpp
src/assorthead/include/chihaya/utils_comparison.hpp
src/assorthead/include/chihaya/utils_dimnames.hpp
src/assorthead/include/chihaya/utils_list.hpp
src/assorthead/include/chihaya/utils_logic.hpp
src/assorthead/include/chihaya/utils_misc.hpp
src/assorthead/include/chihaya/utils_public.hpp
src/assorthead/include/chihaya/utils_subset.hpp
src/assorthead/include/chihaya/utils_type.hpp
src/assorthead/include/chihaya/utils_unary.hpp
src/assorthead/include/chihaya/validate.hpp
src/assorthead/include/clrm1/clrm1.hpp
src/assorthead/include/gsdecon/Options.hpp
src/assorthead/include/gsdecon/Results.hpp
src/assorthead/include/gsdecon/blocked.hpp
src/assorthead/include/gsdecon/compute.hpp
src/assorthead/include/gsdecon/gsdecon.hpp
src/assorthead/include/gsdecon/utils.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/stop_condition.h
src/assorthead/include/hnswlib/visited_list_pool.h
src/assorthead/include/irlba/MockMatrix.hpp
src/assorthead/include/irlba/Options.hpp
src/assorthead/include/irlba/compute.hpp
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/kaori/BarcodePool.hpp
src/assorthead/include/kaori/BarcodeSearch.hpp
src/assorthead/include/kaori/FastqReader.hpp
src/assorthead/include/kaori/MismatchTrie.hpp
src/assorthead/include/kaori/ScanTemplate.hpp
src/assorthead/include/kaori/SimpleSingleMatch.hpp
src/assorthead/include/kaori/kaori.hpp
src/assorthead/include/kaori/process_data.hpp
src/assorthead/include/kaori/utils.hpp
src/assorthead/include/kaori/handlers/CombinatorialBarcodesPairedEnd.hpp
src/assorthead/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp
src/assorthead/include/kaori/handlers/DualBarcodesPairedEnd.hpp
src/assorthead/include/kaori/handlers/DualBarcodesPairedEndWithDiagnostics.hpp
src/assorthead/include/kaori/handlers/DualBarcodesSingleEnd.hpp
src/assorthead/include/kaori/handlers/DualBarcodesSingleEndWithDiagnostics.hpp
src/assorthead/include/kaori/handlers/RandomBarcodeSingleEnd.hpp
src/assorthead/include/kaori/handlers/SingleBarcodePairedEnd.hpp
src/assorthead/include/kaori/handlers/SingleBarcodeSingleEnd.hpp
src/assorthead/include/kmeans/Details.hpp
src/assorthead/include/kmeans/Initialize.hpp
src/assorthead/include/kmeans/InitializeKmeanspp.hpp
src/assorthead/include/kmeans/InitializeNone.hpp
src/assorthead/include/kmeans/InitializeRandom.hpp
src/assorthead/include/kmeans/InitializeVariancePartition.hpp
src/assorthead/include/kmeans/MockMatrix.hpp
src/assorthead/include/kmeans/QuickSearch.hpp
src/assorthead/include/kmeans/Refine.hpp
src/assorthead/include/kmeans/RefineHartiganWong.hpp
src/assorthead/include/kmeans/RefineLloyd.hpp
src/assorthead/include/kmeans/RefineMiniBatch.hpp
src/assorthead/include/kmeans/SimpleMatrix.hpp
src/assorthead/include/kmeans/compute_centroids.hpp
src/assorthead/include/kmeans/compute_wcss.hpp
src/assorthead/include/kmeans/copy_into_array.hpp
src/assorthead/include/kmeans/is_edge_case.hpp
src/assorthead/include/kmeans/kmeans.hpp
src/assorthead/include/kmeans/parallelize.hpp
src/assorthead/include/knncolle/Bruteforce.hpp
src/assorthead/include/knncolle/Builder.hpp
src/assorthead/include/knncolle/Kmknn.hpp
src/assorthead/include/knncolle/L2Normalized.hpp
src/assorthead/include/knncolle/MockMatrix.hpp
src/assorthead/include/knncolle/NeighborQueue.hpp
src/assorthead/include/knncolle/Prebuilt.hpp
src/assorthead/include/knncolle/Searcher.hpp
src/assorthead/include/knncolle/Vptree.hpp
src/assorthead/include/knncolle/distances.hpp
src/assorthead/include/knncolle/find_nearest_neighbors.hpp
src/assorthead/include/knncolle/knncolle.hpp
src/assorthead/include/knncolle/report_all_neighbors.hpp
src/assorthead/include/knncolle_annoy/knncolle_annoy.hpp
src/assorthead/include/knncolle_hnsw/distances.hpp
src/assorthead/include/knncolle_hnsw/knncolle_hnsw.hpp
src/assorthead/include/manticore/manticore.hpp
src/assorthead/include/millijson/millijson.hpp
src/assorthead/include/mnncorrect/AutomaticOrder.hpp
src/assorthead/include/mnncorrect/CustomOrder.hpp
src/assorthead/include/mnncorrect/Options.hpp
src/assorthead/include/mnncorrect/ReferencePolicy.hpp
src/assorthead/include/mnncorrect/compute.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/mnncorrect.hpp
src/assorthead/include/mnncorrect/parallelize.hpp
src/assorthead/include/mnncorrect/restore_order.hpp
src/assorthead/include/mnncorrect/robust_average.hpp
src/assorthead/include/mnncorrect/utils.hpp
src/assorthead/include/mumosa/mumosa.hpp
src/assorthead/include/nenesub/nenesub.hpp
src/assorthead/include/phyper/phyper.hpp
src/assorthead/include/powerit/core.hpp
src/assorthead/include/powerit/powerit.hpp
src/assorthead/include/powerit/simple.hpp
src/assorthead/include/qdtsne/Options.hpp
src/assorthead/include/qdtsne/SPTree.hpp
src/assorthead/include/qdtsne/Status.hpp
src/assorthead/include/qdtsne/gaussian.hpp
src/assorthead/include/qdtsne/initialize.hpp
src/assorthead/include/qdtsne/qdtsne.hpp
src/assorthead/include/qdtsne/symmetrize.hpp
src/assorthead/include/qdtsne/utils.hpp
src/assorthead/include/raiigraph/Graph.hpp
src/assorthead/include/raiigraph/Matrix.hpp
src/assorthead/include/raiigraph/RNGScope.hpp
src/assorthead/include/raiigraph/Vector.hpp
src/assorthead/include/raiigraph/error.hpp
src/assorthead/include/raiigraph/raiigraph.hpp
src/assorthead/include/raiigraph/fragments/matrix.hpp
src/assorthead/include/raiigraph/fragments/vector.hpp
src/assorthead/include/rds2cpp/Environment.hpp
src/assorthead/include/rds2cpp/ExternalPointer.hpp
src/assorthead/include/rds2cpp/RObject.hpp
src/assorthead/include/rds2cpp/RdsFile.hpp
src/assorthead/include/rds2cpp/SEXPType.hpp
src/assorthead/include/rds2cpp/SharedParseInfo.hpp
src/assorthead/include/rds2cpp/SharedWriteInfo.hpp
src/assorthead/include/rds2cpp/StringEncoding.hpp
src/assorthead/include/rds2cpp/Symbol.hpp
src/assorthead/include/rds2cpp/parse_altrep.hpp
src/assorthead/include/rds2cpp/parse_atomic.hpp
src/assorthead/include/rds2cpp/parse_attributes.hpp
src/assorthead/include/rds2cpp/parse_builtin.hpp
src/assorthead/include/rds2cpp/parse_environment.hpp
src/assorthead/include/rds2cpp/parse_expression.hpp
src/assorthead/include/rds2cpp/parse_external_pointer.hpp
src/assorthead/include/rds2cpp/parse_language.hpp
src/assorthead/include/rds2cpp/parse_list.hpp
src/assorthead/include/rds2cpp/parse_object.hpp
src/assorthead/include/rds2cpp/parse_pairlist.hpp
src/assorthead/include/rds2cpp/parse_rds.hpp
src/assorthead/include/rds2cpp/parse_s4.hpp
src/assorthead/include/rds2cpp/parse_single_string.hpp
src/assorthead/include/rds2cpp/parse_symbol.hpp
src/assorthead/include/rds2cpp/rds2cpp.hpp
src/assorthead/include/rds2cpp/utils_parse.hpp
src/assorthead/include/rds2cpp/utils_write.hpp
src/assorthead/include/rds2cpp/write_atomic.hpp
src/assorthead/include/rds2cpp/write_attributes.hpp
src/assorthead/include/rds2cpp/write_builtin.hpp
src/assorthead/include/rds2cpp/write_expression.hpp
src/assorthead/include/rds2cpp/write_language.hpp
src/assorthead/include/rds2cpp/write_list.hpp
src/assorthead/include/rds2cpp/write_object.hpp
src/assorthead/include/rds2cpp/write_pairlist.hpp
src/assorthead/include/rds2cpp/write_rds.hpp
src/assorthead/include/rds2cpp/write_s4.hpp
src/assorthead/include/rds2cpp/write_single_string.hpp
src/assorthead/include/ritsuko/choose_missing_placeholder.hpp
src/assorthead/include/ritsuko/find_extremes.hpp
src/assorthead/include/ritsuko/is_date_time.hpp
src/assorthead/include/ritsuko/parse_version_string.hpp
src/assorthead/include/ritsuko/r_missing_value.hpp
src/assorthead/include/ritsuko/ritsuko.hpp
src/assorthead/include/ritsuko/hdf5/IterateNdDataset.hpp
src/assorthead/include/ritsuko/hdf5/Stream1dNumericDataset.hpp
src/assorthead/include/ritsuko/hdf5/Stream1dStringDataset.hpp
src/assorthead/include/ritsuko/hdf5/_strings.hpp
src/assorthead/include/ritsuko/hdf5/as_numeric_datatype.hpp
src/assorthead/include/ritsuko/hdf5/exceeds_limit.hpp
src/assorthead/include/ritsuko/hdf5/get_1d_length.hpp
src/assorthead/include/ritsuko/hdf5/get_dimensions.hpp
src/assorthead/include/ritsuko/hdf5/get_name.hpp
src/assorthead/include/ritsuko/hdf5/hdf5.hpp
src/assorthead/include/ritsuko/hdf5/is_utf8_string.hpp
src/assorthead/include/ritsuko/hdf5/load_attribute.hpp
src/assorthead/include/ritsuko/hdf5/load_dataset.hpp
src/assorthead/include/ritsuko/hdf5/miscellaneous.hpp
src/assorthead/include/ritsuko/hdf5/missing_placeholder.hpp
src/assorthead/include/ritsuko/hdf5/open.hpp
src/assorthead/include/ritsuko/hdf5/pick_1d_block_size.hpp
src/assorthead/include/ritsuko/hdf5/pick_nd_block_dimensions.hpp
src/assorthead/include/ritsuko/hdf5/validate_string.hpp
src/assorthead/include/scran_aggregate/aggregate_across_cells.hpp
src/assorthead/include/scran_aggregate/aggregate_across_genes.hpp
src/assorthead/include/scran_aggregate/clean_factor.hpp
src/assorthead/include/scran_aggregate/combine_factors.hpp
src/assorthead/include/scran_aggregate/scran_aggregate.hpp
src/assorthead/include/scran_blocks/average_vectors.hpp
src/assorthead/include/scran_blocks/block_weights.hpp
src/assorthead/include/scran_blocks/scran_blocks.hpp
src/assorthead/include/scran_graph_cluster/build_snn_graph.hpp
src/assorthead/include/scran_graph_cluster/cluster_leiden.hpp
src/assorthead/include/scran_graph_cluster/cluster_multilevel.hpp
src/assorthead/include/scran_graph_cluster/cluster_walktrap.hpp
src/assorthead/include/scran_graph_cluster/edges_to_graph.hpp
src/assorthead/include/scran_graph_cluster/scran_graph_cluster.hpp
src/assorthead/include/scran_markers/PrecomputedPairwiseWeights.hpp
src/assorthead/include/scran_markers/auc.hpp
src/assorthead/include/scran_markers/average_group_stats.hpp
src/assorthead/include/scran_markers/cohens_d.hpp
src/assorthead/include/scran_markers/create_combinations.hpp
src/assorthead/include/scran_markers/scan_matrix.hpp
src/assorthead/include/scran_markers/score_markers_pairwise.hpp
src/assorthead/include/scran_markers/score_markers_summary.hpp
src/assorthead/include/scran_markers/scran_markers.hpp
src/assorthead/include/scran_markers/simple_diff.hpp
src/assorthead/include/scran_markers/summarize_comparisons.hpp
src/assorthead/include/scran_markers/summarize_effects.hpp
src/assorthead/include/scran_norm/center_size_factors.hpp
src/assorthead/include/scran_norm/choose_pseudo_count.hpp
src/assorthead/include/scran_norm/normalize_counts.hpp
src/assorthead/include/scran_norm/sanitize_size_factors.hpp
src/assorthead/include/scran_norm/scran_norm.hpp
src/assorthead/include/scran_pca/blocked_pca.hpp
src/assorthead/include/scran_pca/scran_pca.hpp
src/assorthead/include/scran_pca/simple_pca.hpp
src/assorthead/include/scran_pca/utils.hpp
src/assorthead/include/scran_qc/adt_quality_control.hpp
src/assorthead/include/scran_qc/choose_filter_thresholds.hpp
src/assorthead/include/scran_qc/crispr_quality_control.hpp
src/assorthead/include/scran_qc/find_median_mad.hpp
src/assorthead/include/scran_qc/format_filters.hpp
src/assorthead/include/scran_qc/per_cell_qc_metrics.hpp
src/assorthead/include/scran_qc/rna_quality_control.hpp
src/assorthead/include/scran_qc/scran_qc.hpp
src/assorthead/include/scran_variances/choose_highly_variable_genes.hpp
src/assorthead/include/scran_variances/fit_variance_trend.hpp
src/assorthead/include/scran_variances/model_gene_variances.hpp
src/assorthead/include/scran_variances/scran_variances.hpp
src/assorthead/include/singlepp/Intersection.hpp
src/assorthead/include/singlepp/Markers.hpp
src/assorthead/include/singlepp/SubsetRemapper.hpp
src/assorthead/include/singlepp/SubsetSanitizer.hpp
src/assorthead/include/singlepp/annotate_cells_integrated.hpp
src/assorthead/include/singlepp/annotate_cells_single.hpp
src/assorthead/include/singlepp/build_indices.hpp
src/assorthead/include/singlepp/choose_classic_markers.hpp
src/assorthead/include/singlepp/classify_integrated.hpp
src/assorthead/include/singlepp/classify_single.hpp
src/assorthead/include/singlepp/correlations_to_score.hpp
src/assorthead/include/singlepp/defs.hpp
src/assorthead/include/singlepp/fill_labels_in_use.hpp
src/assorthead/include/singlepp/find_best_and_delta.hpp
src/assorthead/include/singlepp/scaled_ranks.hpp
src/assorthead/include/singlepp/singlepp.hpp
src/assorthead/include/singlepp/subset_to_markers.hpp
src/assorthead/include/singlepp/train_integrated.hpp
src/assorthead/include/singlepp/train_single.hpp
src/assorthead/include/subpar/range.hpp
src/assorthead/include/subpar/simple.hpp
src/assorthead/include/subpar/subpar.hpp
src/assorthead/include/subpar/test.hpp
src/assorthead/include/takane/_derived_from.hpp
src/assorthead/include/takane/_dimensions.hpp
src/assorthead/include/takane/_height.hpp
src/assorthead/include/takane/_satisfies_interface.hpp
src/assorthead/include/takane/_validate.hpp
src/assorthead/include/takane/atomic_vector.hpp
src/assorthead/include/takane/atomic_vector_list.hpp
src/assorthead/include/takane/bam_file.hpp
src/assorthead/include/takane/bcf_file.hpp
src/assorthead/include/takane/bed_file.hpp
src/assorthead/include/takane/bigbed_file.hpp
src/assorthead/include/takane/bigwig_file.hpp
src/assorthead/include/takane/bumpy_atomic_array.hpp
src/assorthead/include/takane/bumpy_data_frame_array.hpp
src/assorthead/include/takane/compressed_sparse_matrix.hpp
src/assorthead/include/takane/csv_data_frame.hpp
src/assorthead/include/takane/data_frame.hpp
src/assorthead/include/takane/data_frame_factor.hpp
src/assorthead/include/takane/data_frame_list.hpp
src/assorthead/include/takane/delayed_array.hpp
src/assorthead/include/takane/dense_array.hpp
src/assorthead/include/takane/fasta_file.hpp
src/assorthead/include/takane/fastq_file.hpp
src/assorthead/include/takane/genomic_ranges.hpp
src/assorthead/include/takane/genomic_ranges_list.hpp
src/assorthead/include/takane/gff_file.hpp
src/assorthead/include/takane/gmt_file.hpp
src/assorthead/include/takane/multi_sample_dataset.hpp
src/assorthead/include/takane/ranged_summarized_experiment.hpp
src/assorthead/include/takane/rds_file.hpp
src/assorthead/include/takane/sequence_information.hpp
src/assorthead/include/takane/sequence_string_set.hpp
src/assorthead/include/takane/simple_list.hpp
src/assorthead/include/takane/single_cell_experiment.hpp
src/assorthead/include/takane/spatial_experiment.hpp
src/assorthead/include/takane/string_factor.hpp
src/assorthead/include/takane/summarized_experiment.hpp
src/assorthead/include/takane/takane.hpp
src/assorthead/include/takane/utils_array.hpp
src/assorthead/include/takane/utils_bumpy_array.hpp
src/assorthead/include/takane/utils_compressed_list.hpp
src/assorthead/include/takane/utils_csv.hpp
src/assorthead/include/takane/utils_factor.hpp
src/assorthead/include/takane/utils_files.hpp
src/assorthead/include/takane/utils_json.hpp
src/assorthead/include/takane/utils_other.hpp
src/assorthead/include/takane/utils_public.hpp
src/assorthead/include/takane/utils_string.hpp
src/assorthead/include/takane/utils_summarized_experiment.hpp
src/assorthead/include/takane/vcf_experiment.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/Oracle.hpp
src/assorthead/include/tatami/base/SparseRange.hpp
src/assorthead/include/tatami/dense/DenseMatrix.hpp
src/assorthead/include/tatami/dense/SparsifiedWrapper.hpp
src/assorthead/include/tatami/dense/convert_to_dense.hpp
src/assorthead/include/tatami/dense/transpose.hpp
src/assorthead/include/tatami/isometric/arithmetic_utils.hpp
src/assorthead/include/tatami/isometric/boolean_utils.hpp
src/assorthead/include/tatami/isometric/compare_utils.hpp
src/assorthead/include/tatami/isometric/depends_utils.hpp
src/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp
src/assorthead/include/tatami/isometric/binary/arithmetic_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/mock_helpers.hpp
src/assorthead/include/tatami/isometric/binary/utils.hpp
src/assorthead/include/tatami/isometric/unary/DelayedUnaryIsometricOperation.hpp
src/assorthead/include/tatami/isometric/unary/arithmetic_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/isometric/unary/mock_helpers.hpp
src/assorthead/include/tatami/isometric/unary/substitute_helpers.hpp
src/assorthead/include/tatami/other/ConstantMatrix.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/compress_sparse_triplets.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/secondary_extraction.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/ConsecutiveOracle.hpp
src/assorthead/include/tatami/utils/ElementType.hpp
src/assorthead/include/tatami/utils/FixedOracle.hpp
src/assorthead/include/tatami/utils/PseudoOracularExtractor.hpp
src/assorthead/include/tatami/utils/SomeNumericArray.hpp
src/assorthead/include/tatami/utils/consecutive_extractor.hpp
src/assorthead/include/tatami/utils/copy.hpp
src/assorthead/include/tatami/utils/has_data.hpp
src/assorthead/include/tatami/utils/new_extractor.hpp
src/assorthead/include/tatami/utils/parallelize.hpp
src/assorthead/include/tatami/utils/process_consecutive_indices.hpp
src/assorthead/include/tatami/utils/wrap_shared_ptr.hpp
src/assorthead/include/tatami_chunked/ChunkDimensionStats.hpp
src/assorthead/include/tatami_chunked/CustomDenseChunkedMatrix.hpp
src/assorthead/include/tatami_chunked/CustomSparseChunkedMatrix.hpp
src/assorthead/include/tatami_chunked/DenseSlabFactory.hpp
src/assorthead/include/tatami_chunked/LruSlabCache.hpp
src/assorthead/include/tatami_chunked/OracularSlabCache.hpp
src/assorthead/include/tatami_chunked/OracularSubsettedSlabCache.hpp
src/assorthead/include/tatami_chunked/OracularVariableSlabCache.hpp
src/assorthead/include/tatami_chunked/SlabCacheStats.hpp
src/assorthead/include/tatami_chunked/SparseSlabFactory.hpp
src/assorthead/include/tatami_chunked/custom_internals.hpp
src/assorthead/include/tatami_chunked/mock_dense_chunk.hpp
src/assorthead/include/tatami_chunked/mock_sparse_chunk.hpp
src/assorthead/include/tatami_chunked/tatami_chunked.hpp
src/assorthead/include/tatami_hdf5/CompressedSparseMatrix.hpp
src/assorthead/include/tatami_hdf5/DenseMatrix.hpp
src/assorthead/include/tatami_hdf5/load_compressed_sparse_matrix.hpp
src/assorthead/include/tatami_hdf5/load_dense_matrix.hpp
src/assorthead/include/tatami_hdf5/serialize.hpp
src/assorthead/include/tatami_hdf5/sparse_primary.hpp
src/assorthead/include/tatami_hdf5/sparse_secondary.hpp
src/assorthead/include/tatami_hdf5/tatami_hdf5.hpp
src/assorthead/include/tatami_hdf5/utils.hpp
src/assorthead/include/tatami_hdf5/write_compressed_sparse_matrix.hpp
src/assorthead/include/tatami_mult/dense_column.hpp
src/assorthead/include/tatami_mult/dense_row.hpp
src/assorthead/include/tatami_mult/sparse_column.hpp
src/assorthead/include/tatami_mult/sparse_row.hpp
src/assorthead/include/tatami_mult/tatami_mult.hpp
src/assorthead/include/tatami_mult/utils.hpp
src/assorthead/include/tatami_r/UnknownMatrix.hpp
src/assorthead/include/tatami_r/dense_extractor.hpp
src/assorthead/include/tatami_r/dense_matrix.hpp
src/assorthead/include/tatami_r/parallelize.hpp
src/assorthead/include/tatami_r/sparse_extractor.hpp
src/assorthead/include/tatami_r/sparse_matrix.hpp
src/assorthead/include/tatami_r/tatami_r.hpp
src/assorthead/include/tatami_r/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/grouped_variances.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/tatami_stats.hpp
src/assorthead/include/tatami_stats/utils.hpp
src/assorthead/include/tatami_stats/variances.hpp
src/assorthead/include/tatami_tiledb/DenseMatrix.hpp
src/assorthead/include/tatami_tiledb/SparseMatrix.hpp
src/assorthead/include/tatami_tiledb/serialize.hpp
src/assorthead/include/tatami_tiledb/tatami_tiledb.hpp
src/assorthead/include/tatami_tiledb/utils.hpp
src/assorthead/include/umappp/NeighborList.hpp
src/assorthead/include/umappp/Options.hpp
src/assorthead/include/umappp/Status.hpp
src/assorthead/include/umappp/combine_neighbor_sets.hpp
src/assorthead/include/umappp/find_ab.hpp
src/assorthead/include/umappp/initialize.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
src/assorthead/include/uzuki2/Dummy.hpp
src/assorthead/include/uzuki2/ExternalTracker.hpp
src/assorthead/include/uzuki2/ParsedList.hpp
src/assorthead/include/uzuki2/Version.hpp
src/assorthead/include/uzuki2/interfaces.hpp
src/assorthead/include/uzuki2/parse_hdf5.hpp
src/assorthead/include/uzuki2/parse_json.hpp
src/assorthead/include/uzuki2/uzuki2.hpp
src/assorthead/licenses/Eigen/COPYING.APACHE
src/assorthead/licenses/Eigen/COPYING.BSD
src/assorthead/licenses/Eigen/COPYING.GPL
src/assorthead/licenses/Eigen/COPYING.LGPL
src/assorthead/licenses/Eigen/COPYING.MINPACK
src/assorthead/licenses/Eigen/COPYING.MPL2
src/assorthead/licenses/Eigen/COPYING.README
src/assorthead/licenses/WeightedLowess/LICENSE
src/assorthead/licenses/aarand/LICENSE
src/assorthead/licenses/annoy/LICENSE
src/assorthead/licenses/byteme/LICENSE
src/assorthead/licenses/chihaya/LICENSE
src/assorthead/licenses/clrm1/LICENSE
src/assorthead/licenses/gsdecon/LICENSE
src/assorthead/licenses/hnswlib/LICENSE
src/assorthead/licenses/irlba/LICENSE
src/assorthead/licenses/kaori/LICENSE
src/assorthead/licenses/kmeans/LICENSE
src/assorthead/licenses/knncolle/LICENSE
src/assorthead/licenses/knncolle_annoy/LICENSE
src/assorthead/licenses/knncolle_hnsw/LICENSE
src/assorthead/licenses/manticore/LICENSE
src/assorthead/licenses/millijson/LICENSE
src/assorthead/licenses/mnncorrect/LICENSE
src/assorthead/licenses/mumosa/LICENSE
src/assorthead/licenses/nenesub/LICENSE
src/assorthead/licenses/phyper/LICENSE
src/assorthead/licenses/powerit/LICENSE
src/assorthead/licenses/qdtsne/LICENSE
src/assorthead/licenses/raiigraph/LICENSE
src/assorthead/licenses/rds2cpp/LICENSE
src/assorthead/licenses/ritsuko/LICENSE
src/assorthead/licenses/scran_aggregate/LICENSE
src/assorthead/licenses/scran_blocks/LICENSE
src/assorthead/licenses/scran_graph_cluster/LICENSE
src/assorthead/licenses/scran_markers/LICENSE
src/assorthead/licenses/scran_norm/LICENSE
src/assorthead/licenses/scran_pca/LICENSE
src/assorthead/licenses/scran_qc/LICENSE
src/assorthead/licenses/scran_variances/LICENSE
src/assorthead/licenses/singlepp/LICENSE
src/assorthead/licenses/subpar/LICENSE
src/assorthead/licenses/takane/LICENSE
src/assorthead/licenses/tatami/LICENSE
src/assorthead/licenses/tatami_chunked/LICENSE
src/assorthead/licenses/tatami_hdf5/LICENSE
src/assorthead/licenses/tatami_mult/LICENSE
src/assorthead/licenses/tatami_r/LICENSE
src/assorthead/licenses/tatami_stats/LICENSE
src/assorthead/licenses/tatami_tiledb/LICENSE
src/assorthead/licenses/umappp/LICENSE
src/assorthead/licenses/uzuki2/LICENSE
tests/conftest.py
tests/test_includes.py