AGENTS.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
uv.lock
bin/sgtsne
scarf/__init__.py
scarf/_version.py
scarf/cytebase.py
scarf/lineage.py
scarf.egg-info/PKG-INFO
scarf.egg-info/SOURCES.txt
scarf.egg-info/dependency_links.txt
scarf.egg-info/requires.txt
scarf.egg-info/scm_file_list.json
scarf.egg-info/scm_version.json
scarf.egg-info/top_level.txt
scarf/assay/__init__.py
scarf/assay/adt.py
scarf/assay/atac.py
scarf/assay/base.py
scarf/assay/normalization.py
scarf/assay/persistence.py
scarf/assay/rna.py
scarf/clustering/__init__.py
scarf/clustering/_paris_core.py
scarf/clustering/_paris_modularity.py
scarf/clustering/balanced_cut.py
scarf/clustering/cluster_tree.py
scarf/clustering/leiden.py
scarf/clustering/paris.py
scarf/clustering/paris_multiscale.py
scarf/datastore/__init__.py
scarf/datastore/_plot_accessor.py
scarf/datastore/base_datastore.py
scarf/datastore/datastore.py
scarf/datastore/graph_datastore.py
scarf/datastore/mapping_datastore.py
scarf/datastore/pipeline_accessor.py
scarf/datastore/plot_accessor.py
scarf/datastore/summary.py
scarf/datastore/_operations/__init__.py
scarf/datastore/_operations/clustering.py
scarf/datastore/_operations/embeddings.py
scarf/datastore/_operations/enrichment_store.py
scarf/datastore/_operations/features.py
scarf/datastore/_operations/graph.py
scarf/datastore/_operations/integration_metrics.py
scarf/datastore/_operations/mapping.py
scarf/datastore/_operations/mapping_reference.py
scarf/datastore/_operations/paris_persistence.py
scarf/datastore/_operations/presentation.py
scarf/datastore/_operations/quality_control.py
scarf/datastore/_operations/trajectory.py
scarf/embeddings/__init__.py
scarf/embeddings/imported.py
scarf/embeddings/initialization.py
scarf/embeddings/reduction.py
scarf/embeddings/sgtsne.py
scarf/embeddings/umap.py
scarf/embeddings/harmony/__init__.py
scarf/embeddings/harmony/api.py
scarf/embeddings/harmony/models.py
scarf/embeddings/harmony/optimizer.py
scarf/features/__init__.py
scarf/features/scoring.py
scarf/features/variability.py
scarf/features/enrichment/__init__.py
scarf/features/enrichment/aucell.py
scarf/features/enrichment/net.py
scarf/features/enrichment/results.py
scarf/features/enrichment/waggr.py
scarf/features/genomic/__init__.py
scarf/features/genomic/gff.py
scarf/features/genomic/intervals.py
scarf/features/genomic/melding.py
scarf/features/markers/__init__.py
scarf/features/markers/batching.py
scarf/features/markers/correction.py
scarf/features/markers/rank.py
scarf/features/markers/regression.py
scarf/features/markers/search.py
scarf/features/markers/table.py
scarf/graph/__init__.py
scarf/graph/arguments.py
scarf/graph/distances.py
scarf/graph/encoded_paths.py
scarf/graph/paths.py
scarf/graph/state.py
scarf/mapping/__init__.py
scarf/mapping/artifact.py
scarf/mapping/confidence.py
scarf/mapping/features.py
scarf/mapping/hashing.py
scarf/mapping/models.py
scarf/mapping/projection.py
scarf/mapping/reference.py
scarf/mapping/symphony.py
scarf/matrix/__init__.py
scarf/matrix/_indexing.py
scarf/matrix/_operations.py
scarf/matrix/_reductions.py
scarf/matrix/blocks.py
scarf/matrix/chunked.py
scarf/merge/__init__.py
scarf/merge/datasets.py
scarf/merge/features.py
scarf/merge/metadata.py
scarf/merge/models.py
scarf/merge/row_plan.py
scarf/merge/writer.py
scarf/metadata/__init__.py
scarf/metadata/arguments.py
scarf/metadata/artifacts.py
scarf/metadata/queries.py
scarf/metadata/rows.py
scarf/metadata/table.py
scarf/metrics/__init__.py
scarf/metrics/_rows.py
scarf/metrics/_types.py
scarf/metrics/cluster_separability.py
scarf/metrics/concordance.py
scarf/metrics/connectivity.py
scarf/metrics/graph.py
scarf/metrics/lisi.py
scarf/metrics/silhouette.py
scarf/neighbors/__init__.py
scarf/neighbors/diffusion.py
scarf/neighbors/graph.py
scarf/neighbors/index.py
scarf/neighbors/integration.py
scarf/neighbors/stages.py
scarf/neighbors/stream.py
scarf/plotting/__init__.py
scarf/plotting/_contracts.py
scarf/plotting/_data.py
scarf/plotting/_deps.py
scarf/plotting/_display.py
scarf/plotting/_figure.py
scarf/plotting/_heatmap_utils.py
scarf/plotting/_raster.py
scarf/plotting/_style.py
scarf/plotting/cluster_connectivity.py
scarf/plotting/cluster_tree.py
scarf/plotting/composition.py
scarf/plotting/diagnostics.py
scarf/plotting/distribution.py
scarf/plotting/embedding.py
scarf/plotting/embedding_raster.py
scarf/plotting/heatmaps.py
scarf/plotting/mapping.py
scarf/plotting/recipes.py
scarf/plotting/summary.py
scarf/quality_control/__init__.py
scarf/quality_control/cell_cycle.py
scarf/quality_control/cell_cycle_genes.py
scarf/quality_control/doublets.py
scarf/quality_control/filtering.py
scarf/quality_control/hto.py
scarf/readers/__init__.py
scarf/readers/_assay_names.py
scarf/readers/_h5ad_inspect.py
scarf/readers/_text.py
scarf/readers/cellranger.py
scarf/readers/csv.py
scarf/readers/h5ad.py
scarf/readers/loom.py
scarf/readers/mtx.py
scarf/readers/seurat.py
scarf/readers/_rds/__init__.py
scarf/readers/_rds/_lazy.py
scarf/readers/_rds/_model.py
scarf/readers/_rds/_parser.py
scarf/readers/_rds/_storage.py
scarf/readers/_rds/_types.py
scarf/readers/_seurat/__init__.py
scarf/readers/_seurat/bpcells.py
scarf/readers/_seurat/errors.py
scarf/readers/_seurat/factory.py
scarf/readers/_seurat/fragments.py
scarf/readers/_seurat/hdf5.py
scarf/readers/_seurat/operations.py
scarf/readers/_seurat/paths.py
scarf/readers/_seurat/sources.py
scarf/storage/__init__.py
scarf/storage/ann_index.py
scarf/storage/arrays.py
scarf/storage/artifact_writer.py
scarf/storage/artifacts.py
scarf/storage/budget.py
scarf/storage/copy.py
scarf/storage/feature_stream.py
scarf/storage/geometry.py
scarf/storage/layout.py
scarf/storage/materialize.py
scarf/storage/parallel.py
scarf/storage/partition.py
scarf/storage/profiles.py
scarf/storage/refs.py
scarf/storage/schema.py
scarf/storage/selections.py
scarf/storage/sharding.py
scarf/storage/stores.py
scarf/storage/types.py
scarf/tools/__init__.py
scarf/tools/repack_zarr.py
scarf/trajectory/__init__.py
scarf/trajectory/fate.py
scarf/trajectory/feature_dynamics.py
scarf/trajectory/pseudotime.py
scarf/trajectory/results.py
scarf/utils/__init__.py
scarf/utils/arrays.py
scarf/utils/compute.py
scarf/utils/logging.py
scarf/utils/numba.py
scarf/utils/prefetch.py
scarf/utils/process.py
scarf/utils/progress.py
scarf/writers/__init__.py
scarf/writers/_materialize.py
scarf/writers/_store.py
scarf/writers/cellranger.py
scarf/writers/csv.py
scarf/writers/export.py
scarf/writers/h5ad.py
scarf/writers/loom.py
scarf/writers/seurat.py
scarf/writers/sparse.py
scarf/writers/subset.py