├── .cirun.yml ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── submit-question.md └── workflows │ ├── codespell.yml │ ├── docker.yml │ ├── publish.yml │ └── test-gpu.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .taplo.toml ├── LICENSE ├── README.md ├── ci ├── environment.yml └── environment_alpha.yml ├── conda ├── rsc_rapids_25.08.yml └── rsc_rapids_25.10.yml ├── docker ├── Dockerfile ├── Dockerfile.deps └── docker-push.sh ├── docs ├── Installation.md ├── MM.md ├── Makefile ├── Out_of_core.md ├── Usage_Principles.md ├── _static │ ├── css │ │ └── override.css │ ├── logo_RTD.svg │ ├── logo_black.svg │ ├── logo_file_reference.svg │ ├── logo_small.svg │ ├── logo_small_name.svg │ └── logo_white.svg ├── _templates │ └── autosummary │ │ └── class.rst ├── acknowledgements.md ├── api │ ├── decoupler_gpu.md │ ├── get.md │ ├── index.md │ ├── scanpy_gpu.md │ └── squidpy_gpu.md ├── basic.md ├── conf.py ├── index.md ├── make.bat ├── notebooks.rst ├── notebooks │ ├── 01_demo_gpu.ipynb │ ├── 02_decoupler.ipynb │ ├── 03_demo_gpu-PR.ipynb │ ├── 04_spatial_autocorr.ipynb │ ├── 05_out-of-core.ipynb │ ├── 06-multi_gpu_show.ipynb │ ├── demo_gpu-seuratv3-brain-1M.ipynb │ └── ligrec_benchmark.ipynb ├── references.md └── release-notes │ ├── 0.10.0.md │ ├── 0.10.1.md │ ├── 0.10.10.md │ ├── 0.10.11.md │ ├── 0.10.2.md │ ├── 0.10.3.md │ ├── 0.10.4.md │ ├── 0.10.5.md │ ├── 0.10.6.md │ ├── 0.10.7.md │ ├── 0.10.8.md │ ├── 0.10.9.md │ ├── 0.11.0.md │ ├── 0.11.1.md │ ├── 0.12.0.md │ ├── 0.12.1.md │ ├── 0.12.2.md │ ├── 0.12.3.md │ ├── 0.12.4.md │ ├── 0.12.5.md │ ├── 0.12.6.md │ ├── 0.12.7.md │ ├── 0.13.0.md │ ├── 0.13.1.md │ ├── 0.13.2.md │ ├── 0.13.3.md │ ├── 0.13.4.md │ ├── 0.13.5.md │ ├── 0.8.0.md │ ├── 0.8.1.md │ ├── 0.9.0.md │ ├── 0.9.1.md │ ├── 0.9.2.md │ ├── 0.9.3.md │ ├── 0.9.4.md │ ├── 0.9.5.md │ ├── 0.9.6.md │ ├── blank.md │ └── index.md ├── hatch.toml ├── pyproject.toml ├── src ├── rapids_singlecell │ ├── __init__.py │ ├── _compat.py │ ├── _utils │ │ └── __init__.py │ ├── dcg.py │ ├── decoupler_gpu │ │ ├── __init__.py │ │ ├── _helper │ │ │ ├── _Method.py │ │ │ ├── _data.py │ │ │ ├── _docs.py │ │ │ ├── _log.py │ │ │ ├── _net.py │ │ │ ├── _pv.py │ │ │ └── _run.py │ │ ├── _method_aucell.py │ │ ├── _method_mlm.py │ │ ├── _method_ulm.py │ │ ├── _method_waggr.py │ │ └── _method_zscore.py │ ├── get │ │ ├── __init__.py │ │ ├── _aggregated.py │ │ ├── _anndata.py │ │ └── _kernels │ │ │ └── _aggr_kernels.py │ ├── gr.py │ ├── pp.py │ ├── preprocessing │ │ ├── __init__.py │ │ ├── _harmony │ │ │ ├── __init__.py │ │ │ ├── _fuses.py │ │ │ ├── _helper.py │ │ │ └── _kernels │ │ │ │ ├── _kmeans.py │ │ │ │ ├── _normalize.py │ │ │ │ ├── _outer.py │ │ │ │ ├── _pen.py │ │ │ │ └── _scatter_add.py │ │ ├── _harmony_integrate.py │ │ ├── _hvg.py │ │ ├── _kernels │ │ │ ├── _mean_var_kernel.py │ │ │ ├── _norm_kernel.py │ │ │ ├── _pr_kernels.py │ │ │ ├── _qc_kernels.py │ │ │ ├── _qc_kernels_dask.py │ │ │ ├── _scale_kernel.py │ │ │ └── _sparse2dense.py │ │ ├── _neighbors │ │ │ ├── __init__.py │ │ │ ├── _algorithms │ │ │ │ ├── _all_neighbors.py │ │ │ │ ├── _brute.py │ │ │ │ ├── _cagra.py │ │ │ │ ├── _ivfflat.py │ │ │ │ ├── _ivfpq.py │ │ │ │ ├── _kernels │ │ │ │ │ └── _nn_descent.py │ │ │ │ ├── _mg_ivfflat.py │ │ │ │ ├── _mg_ivfpq.py │ │ │ │ └── _nn_descent.py │ │ │ └── _helper │ │ │ │ ├── __init__.py │ │ │ │ └── _kernels │ │ │ │ └── _bbknn.py │ │ ├── _normalize.py │ │ ├── _pca.py │ │ ├── _qc.py │ │ ├── _regress_out.py │ │ ├── _scale.py │ │ ├── _scrublet │ │ │ ├── __init__.py │ │ │ ├── core.py │ │ │ ├── pipeline.py │ │ │ └── sparse_utils.py │ │ ├── _simple.py │ │ ├── _sparse_pca │ │ │ ├── _helper.py │ │ │ ├── _kernels │ │ │ │ └── _pca_sparse_kernel.py │ │ │ └── _sparse_pca.py │ │ └── _utils.py │ ├── squidpy_gpu │ │ ├── __init__.py │ │ ├── _autocorr.py │ │ ├── _co_oc.py │ │ ├── _gearysc.py │ │ ├── _ligrec.py │ │ ├── _moransi.py │ │ ├── _utils.py │ │ └── kernels │ │ │ └── _co_oc.py │ ├── tl.py │ └── tools │ │ ├── __init__.py │ │ ├── _clustering.py │ │ ├── _diffmap.py │ │ ├── _draw_graph.py │ │ ├── _embedding_density.py │ │ ├── _kernels │ │ └── _nan_mean_kernels.py │ │ ├── _pymde.py │ │ ├── _rank_gene_groups.py │ │ ├── _score_genes.py │ │ ├── _tsne.py │ │ ├── _umap.py │ │ └── _utils.py └── testing │ └── rapids_singlecell │ ├── _helper │ └── __init__.py │ └── _pytest │ ├── __init__.py │ └── marks.py └── tests ├── README.md ├── _data ├── dummy.h5ad ├── paul15_means.pickle ├── regress_test_small.npy └── test_data.h5ad ├── _scripts ├── seurat_hvg.csv ├── seurat_hvg_v3.csv.gz └── seurat_hvg_v3_batch.csv ├── dask ├── conftest.py ├── test_dask_aggr.py ├── test_dask_clustering.py ├── test_dask_mean_var.py ├── test_dask_pca.py ├── test_dask_rank_logreg.py ├── test_dask_score_genes.py ├── test_get.py ├── test_hvg_dask.py ├── test_normalize_dask.py ├── test_qc_dask.py └── test_scale_dask.py ├── decoupler ├── conftest.py ├── test_aucell.py ├── test_dc_data.py ├── test_mlm.py ├── 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