LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
include/singlet/pileup/pz_reader.h
include/singlet/pileup/pz_writer.h
include/singlet/pz2/pz2.h
include/singlet/pz2/detail/api.h
include/singlet/pz2/detail/codec2.h
include/singlet/pz2/detail/common.h
include/singlet/pz2/detail/container.h
include/singlet/pz2/detail/isa.h
include/singlet/pz2/detail/rans1.h
include/singlet/pz2/detail/rans1_avx2.h
include/singlet/pz2/detail/rans1_avx512.h
include/singlet/pz2/detail/rans1_dec.h
include/singlet/pz2/detail/rans1_enc.h
include/singlet/pz2/detail/sha256.h
include/singlet/pz2/detail/simd.h
include/singlet/pz2/detail/values.h
python/README.md
python/singlet/__init__.py
python/singlet/__main__.py
python/singlet/_aggregate.py
python/singlet/_ambient_rna_score.py
python/singlet/_annotate.py
python/singlet/_annotate_cell_types.py
python/singlet/_augur_prioritize.py
python/singlet/_auth.py
python/singlet/_batch_evaluation.py
python/singlet/_catalog.py
python/singlet/_cca.py
python/singlet/_cell_communication.py
python/singlet/_cell_cycle.py
python/singlet/_cell_cycle_regression.py
python/singlet/_cell_distances.py
python/singlet/_cell_level_de.py
python/singlet/_cell_type_proportions.py
python/singlet/_cluster_stability.py
python/singlet/_coexpression_modules.py
python/singlet/_combat.py
python/singlet/_composition_analysis.py
python/singlet/_concat.py
python/singlet/_connectivity_score.py
python/singlet/_consensus_clustering.py
python/singlet/_correlation.py
python/singlet/_cross_species_correlation.py
python/singlet/_cv_resolution.py
python/singlet/_de.py
python/singlet/_dendrogram.py
python/singlet/_denoise.py
python/singlet/_describe.py
python/singlet/_differential_abundance.py
python/singlet/_differential_test.py
python/singlet/_diffmap.py
python/singlet/_doublet_score_hybrid.py
python/singlet/_downsample.py
python/singlet/_dpt.py
python/singlet/_draw_graph.py
python/singlet/_embedding_density.py
python/singlet/_enrichr.py
python/singlet/_entropy_score.py
python/singlet/_export_df.py
python/singlet/_fate_probabilities.py
python/singlet/_filter.py
python/singlet/_filter_de.py
python/singlet/_find_all_markers.py
python/singlet/_gene_activity_score.py
python/singlet/_gene_correlation_network.py
python/singlet/_gene_importance.py
python/singlet/_gene_module_score.py
python/singlet/_gene_set_enrichment.py
python/singlet/_gene_set_variation.py
python/singlet/_gene_space_embedding.py
python/singlet/_gene_trend_clustering.py
python/singlet/_harmony.py
python/singlet/_hotspot_genes.py
python/singlet/_hvg.py
python/singlet/_hvg_cell_ranger.py
python/singlet/_hvg_seurat.py
python/singlet/_ica.py
python/singlet/_identify_bipotent_cells.py
python/singlet/_infer_grn.py
python/singlet/_ingest.py
python/singlet/_integrity.py
python/singlet/_io.py
python/singlet/_knn_impute.py
python/singlet/_leiden.py
python/singlet/_loader.py
python/singlet/_louvain.py
python/singlet/_magic.py
python/singlet/_marker_overlap.py
python/singlet/_marker_specificity.py
python/singlet/_metacell.py
python/singlet/_metrics.py
python/singlet/_mnn.py
python/singlet/_morans_i.py
python/singlet/_multiome_factor_analysis.py
python/singlet/_neighbors.py
python/singlet/_nmf.py
python/singlet/_nmf_serve.py
python/singlet/_normalize.py
python/singlet/_optimal_transport.py
python/singlet/_paga.py
python/singlet/_palantir_pseudotime.py
python/singlet/_pca.py
python/singlet/_perturbation_signature.py
python/singlet/_phate.py
python/singlet/_phenograph.py
python/singlet/_plot.py
python/singlet/_plot_embedding.py
python/singlet/_plot_genes_in_groups.py
python/singlet/_plot_heatmap.py
python/singlet/_plot_markers.py
python/singlet/_plot_matrix.py
python/singlet/_plot_paga.py
python/singlet/_plot_ranking.py
python/singlet/_plot_scatter.py
python/singlet/_plot_stacked_violin.py
python/singlet/_plot_tracks.py
python/singlet/_predict_cell_type.py
python/singlet/_pseudobulk.py
python/singlet/_qc.py
python/singlet/_qc_summary.py
python/singlet/_query.py
python/singlet/_rank_genes.py
python/singlet/_recipes.py
python/singlet/_regress.py
python/singlet/_reprogramming_score.py
python/singlet/_restricted.py
python/singlet/_scale.py
python/singlet/_scanorama_integrate.py
python/singlet/_score.py
python/singlet/_scrublet.py
python/singlet/_sparse_pca.py
python/singlet/_spatial.py
python/singlet/_spectral_clustering.py
python/singlet/_splicing_ratio.py
python/singlet/_subcluster.py
python/singlet/_subsample.py
python/singlet/_subsample_balanced.py
python/singlet/_topic_model.py
python/singlet/_trajectory_genes.py
python/singlet/_transfer_labels.py
python/singlet/_transforms.py
python/singlet/_tsne.py
python/singlet/_umap.py
python/singlet/_variance_partition.py
python/singlet/_variational_inference.py
python/singlet/_velocity_pseudotime.py
python/singlet/_versions.py
python/singlet/_weighted_nearest_neighbors.py
python/singlet/_wishart.py
python/singlet/bundle.py
python/singlet/convert.py
python/singlet/fetch.py
python/singlet/find.py
python/singlet/manifest_gen.py
python/singlet/py.typed
python/singlet/whitelists.py
python/singlet.egg-info/PKG-INFO
python/singlet.egg-info/SOURCES.txt
python/singlet.egg-info/dependency_links.txt
python/singlet.egg-info/entry_points.txt
python/singlet.egg-info/requires.txt
python/singlet.egg-info/top_level.txt
python/singlet/atlas/__init__.py
python/singlet/atlas/client.py
python/singlet/celllabels/__init__.py
python/singlet/celllabels/ancestry.py
python/singlet/celllabels/celltype.py
python/singlet/celllabels/evaluate.py
python/singlet/celllabels/guide.py
python/singlet/celllabels/io.py
python/singlet/celllabels/output.py
python/singlet/celllabels/pipeline.py
python/singlet/celllabels/sex.py
python/singlet/celllabels/data/cellguide.json.gz
python/singlet/celllabels/data/cl.json.gz
python/singlet/celllabels/data/human_mouse.tsv.gz
python/singlet/celltype_nn/__init__.py
python/singlet/celltype_nn/benchmark.py
python/singlet/celltype_nn/ensemble.py
python/singlet/celltype_nn/features.py
python/singlet/celltype_nn/model.py
python/singlet/celltype_nn/ontology.py
python/singlet/celltype_nn/output.py
python/singlet/celltype_nn/predict.py
python/singlet/data/catalog_v1.parquet
python/singlet/data/sample_index.parquet
python/singlet/data/whitelists/737K-april-2014.txt
python/singlet/data/whitelists/bd_cls1.txt
python/singlet/data/whitelists/bd_cls2.txt
python/singlet/data/whitelists/bd_cls3.txt
python/singlet/data/whitelists/indrop_bc1.txt
python/singlet/data/whitelists/indrop_bc2.txt
python/singlet/data/whitelists/microwell_bc1_bare.txt
python/singlet/data/whitelists/quartzseq2_bc.txt
python/singlet/data/whitelists/scirna3_rt_bc.txt
python/singlet/data/whitelists/splitseq_bc_rd1.txt
python/singlet/data/whitelists/splitseq_bc_rd2.txt
python/singlet/data/whitelists/splitseq_bc_rd3.txt
python/singlet/derive/__init__.py
python/singlet/derive/gene_counts.py
python/singlet/derive/gene_full.py
python/singlet/derive/pseudobulk.py
python/singlet/derive/psi.py
python/singlet/derive/usa.py
python/singlet/features/__init__.py
python/singlet/features/genesets.py
python/singlet/features/io.py
python/singlet/features/output.py
python/singlet/features/pipeline.py
python/singlet/features/rank.py
python/singlet/features/registry.py
python/singlet/features/data/abundance_human.parquet
python/singlet/features/data/abundance_mouse.parquet
python/singlet/features/data/cell_cycle.json
python/singlet/features/data/hallmark.json
python/singlet/gpu/__init__.py
python/singlet/gpu/_coreutil.py
python/singlet/gpu/version.py
python/singlet/gpu/abundance/__init__.py
python/singlet/gpu/abundance/milo.py
python/singlet/gpu/ase/__init__.py
python/singlet/gpu/ase/daesc.py
python/singlet/gpu/atac/__init__.py
python/singlet/gpu/atac/chromvar.py
python/singlet/gpu/cna/__init__.py
python/singlet/gpu/cna/numbat.py
python/singlet/gpu/comm/__init__.py
python/singlet/gpu/comm/cellchat.py
python/singlet/gpu/de/__init__.py
python/singlet/gpu/de/pseudobulk.py
python/singlet/gpu/disease/__init__.py
python/singlet/gpu/disease/scdrs.py
python/singlet/gpu/enrichment/__init__.py
python/singlet/gpu/enrichment/aucell.py
python/singlet/gpu/enrichment/gsea.py
python/singlet/gpu/enrichment/progeny.py
python/singlet/gpu/enrichment/score_genes.py
python/singlet/gpu/enrichment/ssgsea.py
python/singlet/gpu/eqtl/__init__.py
python/singlet/gpu/eqtl/nebula.py
python/singlet/gpu/fate/__init__.py
python/singlet/gpu/fate/cellrank2.py
python/singlet/gpu/fate/cospar.py
python/singlet/gpu/fate/palantir.py
python/singlet/gpu/generative/__init__.py
python/singlet/gpu/generative/discrete_diffusion.py
python/singlet/gpu/grn/__init__.py
python/singlet/gpu/grn/granie.py
python/singlet/gpu/integrate/__init__.py
python/singlet/gpu/integrate/bbknn.py
python/singlet/gpu/integrate/harmony.py
python/singlet/gpu/io/__init__.py
python/singlet/gpu/io/donor.py
python/singlet/gpu/io/loader.py
python/singlet/gpu/lineage/__init__.py
python/singlet/gpu/lineage/mt.py
python/singlet/gpu/network/__init__.py
python/singlet/gpu/network/hdwgcna.py
python/singlet/gpu/perturbation/__init__.py
python/singlet/gpu/perturbation/perturb_graph.py
python/singlet/gpu/preprocess/__init__.py
python/singlet/gpu/preprocess/hvg.py
python/singlet/gpu/preprocess/lognorm.py
python/singlet/gpu/preprocess/neighbors.py
python/singlet/gpu/preprocess/scale.py
python/singlet/gpu/qc/__init__.py
python/singlet/gpu/qc/doublet_score.py
python/singlet/gpu/qc/omnidoublet.py
python/singlet/gpu/qc/qc_metrics.py
python/singlet/gpu/reduce/__init__.py
python/singlet/gpu/reduce/_nmf_core.py
python/singlet/gpu/reduce/svd.py
python/singlet/gpu/reduce/nmf/__init__.py
python/singlet/gpu/reduce/nmf/csi_gep.py
python/singlet/gpu/spatial/__init__.py
python/singlet/gpu/spatial/cell2fate.py
python/singlet/gpu/spatial/flash_deconv.py
python/singlet/gpu/spatial/stagate.py
python/singlet/gpu/streaming/__init__.py
python/singlet/gpu/streaming/pipeline.py
python/singlet/gpu/tools/__init__.py
python/singlet/gpu/tools/leiden.py
python/singlet/gpu/tools/markers.py
python/singlet/gpu/tools/rank_genes_groups.py
python/singlet/gpu/tools/umap.py
python/singlet/gpu/variants/__init__.py
python/singlet/gpu/variants/monopogen.py
python/singlet/gpu/velocity/__init__.py
python/singlet/gpu/velocity/moments.py
python/singlet/gpu/velocity/velocity.py
python/singlet/io/__init__.py
python/singlet/io/convert.py
python/singlet/mcp/__init__.py
python/singlet/mcp/__main__.py
python/singlet/mcp/server.py
python/singlet/mcp/smoke_test.py
python/singlet/pipeline/__init__.py
python/singlet/pipeline/__main__.py
python/singlet/pipeline/_binary.py
python/singlet/pipeline/_errors.py
python/singlet/pipeline/_run.py
python/singlet/pp/__init__.py
python/singlet/preprocessing/__init__.py
python/singlet/preprocessing/_detect.py
python/singlet/preprocessing/_download.py
python/singlet/preprocessing/_export.py
python/singlet/preprocessing/_qc.py
python/singlet/preprocessing/_quantify.py
python/singlet/preprocessing/_species.py
python/singlet/refbundle/__init__.py
python/singlet/refbundle/_features.py
python/singlet/refbundle/_snp.py
python/singlet/s1/__init__.py
python/singlet/s1/atlas.py
python/singlet/s1/builtin_recipes.py
python/singlet/s1/bundle.py
python/singlet/s1/cellcall.py
python/singlet/s1/cells.py
python/singlet/s1/client.py
python/singlet/s1/codec.py
python/singlet/s1/container.py
python/singlet/s1/context.py
python/singlet/s1/junctions.py
python/singlet/s1/labels.py
python/singlet/s1/labels_step.py
python/singlet/s1/legacy.py
python/singlet/s1/manifest.py
python/singlet/s1/matrix.py
python/singlet/s1/migrate.py
python/singlet/s1/packs.py
python/singlet/s1/packs_build.py
python/singlet/s1/policy.py
python/singlet/s1/rcp_adapter.py
python/singlet/s1/recipes.py
python/singlet/s1/recipes_cells.py
python/singlet/s1/recipes_ctx.py
python/singlet/s1/recipes_extra.py
python/singlet/s1/recipes_mtx.py
python/singlet/s1/recipes_psi.py
python/singlet/s1/recipes_pzw.py
python/singlet/s1/recipes_qc.py
python/singlet/s1/recipes_star.py
python/singlet/s1/recipes_tables.py
python/singlet/s1/recipes_tsv.py
python/singlet/s1/sample.py
python/singlet/s1/sample_facts.py
python/singlet/s1/transport.py
python/singlet/s1/util.py
python/singlet/s1/verify.py
python/singlet/s1/write.py
python/singlet/s1/packs/09243cc59ea1b0223dcbf071e1df34e3.pack
python/singlet/s1/packs/0bcd2ceb31fc6cad695901e449f667cc.pack
python/singlet/s1/packs/15854e80854ce93702dc4c716e6a35c5.pack
python/singlet/s1/packs/32bbdc195ae2486a1257e38d3c4c161e.pack
python/singlet/s1/packs/5b24205cb61a91db46ebbc980e8ee6bc.pack
python/singlet/s1/packs/88579b0570adecbc3f0e8602d65d243f.pack
python/singlet/s1/packs/94e3bff7460f96e92311ff009efae582.pack
python/singlet/s1/packs/99a51e8db8bc54baede2092c8b828737.pack
python/singlet/s1/packs/a34ebca652f38b28f0ab5c0ec2a13249.pack
python/singlet/s1/packs/b3961cb6986f392743ea332b879d1d5a.pack
python/singlet/s1/packs/b6abb72f333412054fd8d2afa76f35b4.pack
python/singlet/s1/packs/b708a9dbd566355a876377babed1a4a1.pack
python/singlet/s1/packs/c46618191a313da3983d934abe51e751.pack
python/singlet/s1/packs/ce5a05fc3282d0e3c39e0c7109619eb1.pack
python/singlet/s1/packs/cef1acaf465ebfc4ff7404f308966e92.pack
python/singlet/s1/packs/fd3fcc82842baa3a1d4c8bc6a8f99b90.pack
python/singlet/s1/packs/index.json
python/singlet/s1/recipes_data/features_order_GRCm39-2024-A.u32.zst
python/singlet/store/__init__.py
python/singlet/store/migrate.py
python/singlet/store/packs_build.py
python/singlet/store/verify.py
python/singlet/torch/__init__.py
python/singlet/torch/_s1stream.py
python/singlet/torch/_stream.py
python/singlet/torch/_torch.py
python/singlet/v2/__init__.py
python/singlet/v2/migrate.py
python/singlet/v2/packs_build.py
python/singlet/v2/verify.py
src/bindings/common/singlet/pz2_client.h
src/bindings/python/_bind_abundance.hpp
src/bindings/python/_bind_ase.hpp
src/bindings/python/_bind_atac.hpp
src/bindings/python/_bind_cna.hpp
src/bindings/python/_bind_comm.hpp
src/bindings/python/_bind_cupy_ingest.hpp
src/bindings/python/_bind_disease.hpp
src/bindings/python/_bind_enrich.hpp
src/bindings/python/_bind_eqtl.hpp
src/bindings/python/_bind_fate.hpp
src/bindings/python/_bind_generative.hpp
src/bindings/python/_bind_grn.hpp
src/bindings/python/_bind_kernels.hpp
src/bindings/python/_bind_loader.hpp
src/bindings/python/_bind_metadata.hpp
src/bindings/python/_bind_network.hpp
src/bindings/python/_bind_nmf_new.hpp
src/bindings/python/_bind_perturbation.hpp
src/bindings/python/_bind_preprocess.hpp
src/bindings/python/_bind_qc_metrics.hpp
src/bindings/python/_bind_qc_new.hpp
src/bindings/python/_bind_results.hpp
src/bindings/python/_bind_score_genes.hpp
src/bindings/python/_bind_spatial_phaseb.hpp
src/bindings/python/_bind_variants.hpp
src/bindings/python/_cupy_interop.hpp
src/bindings/python/_gpu_core.cpp
src/bindings/python/_pz.cpp
src/bindings/python/_pz2.cpp
src/bindings/python/_singlepress.cpp