AGENTS.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
uv.lock
cytearc/__init__.py
cytearc/_facade.py
cytearc/_version.py
cytearc.egg-info/PKG-INFO
cytearc.egg-info/SOURCES.txt
cytearc.egg-info/dependency_links.txt
cytearc.egg-info/requires.txt
cytearc.egg-info/scm_file_list.json
cytearc.egg-info/scm_version.json
cytearc.egg-info/top_level.txt
cytearc/agent/.gitignore
cytearc/agent/README.md
cytearc/agent/VALIDATION.md
cytearc/agent/__init__.py
cytearc/agent/api.py
cytearc/agent/choices.py
cytearc/agent/compact_result.py
cytearc/agent/diagnostics.py
cytearc/agent/evidence.py
cytearc/agent/execution.py
cytearc/agent/models.py
cytearc/agent/plots.py
cytearc/agent/prompts.py
cytearc/agent/provider.py
cytearc/agent/records.py
cytearc/agent/rendering.py
cytearc/agent/report_assets.py
cytearc/agent/report_charts.py
cytearc/agent/report_html.py
cytearc/agent/report_style.py
cytearc/agent/report_text.py
cytearc/agent/result.py
cytearc/agent/workflow.py
cytearc/assay/__init__.py
cytearc/assay/adt.py
cytearc/assay/atac.py
cytearc/assay/base.py
cytearc/assay/classification.py
cytearc/assay/feature_summary.py
cytearc/assay/normalization.py
cytearc/assay/persistence.py
cytearc/assay/rna.py
cytearc/clustering/__init__.py
cytearc/clustering/_paris_core.py
cytearc/clustering/_paris_modularity.py
cytearc/clustering/cluster_tree.py
cytearc/clustering/leiden.py
cytearc/clustering/paris.py
cytearc/clustering/paris_multiscale.py
cytearc/cytebase/__init__.py
cytearc/cytebase/_embeddings.py
cytearc/cytebase/_storage.py
cytearc/cytebase/catalog.py
cytearc/cytebase/connector.py
cytearc/cytebase/display.py
cytearc/cytebase/entry.py
cytearc/cytebase/pipeline/__init__.py
cytearc/cytebase/pipeline/__main__.py
cytearc/cytebase/pipeline/app.py
cytearc/cytebase/pipeline/build.py
cytearc/cytebase/pipeline/catalog.py
cytearc/cytebase/pipeline/deploy.py
cytearc/cytebase/pipeline/download.py
cytearc/cytebase/pipeline/inventory.py
cytearc/cytebase/pipeline/models.py
cytearc/cytebase/pipeline/resources.py
cytearc/cytebase/pipeline/selection.py
cytearc/datastore/__init__.py
cytearc/datastore/_pipeline_cluster_selection.py
cytearc/datastore/_pipeline_fields.py
cytearc/datastore/_pipeline_filtering.py
cytearc/datastore/_pipeline_ledger.py
cytearc/datastore/_pipeline_recipe.py
cytearc/datastore/_plot_accessor.py
cytearc/datastore/artifact_accessor.py
cytearc/datastore/base_datastore.py
cytearc/datastore/datastore.py
cytearc/datastore/graph_datastore.py
cytearc/datastore/mapping_datastore.py
cytearc/datastore/namespaces.py
cytearc/datastore/pipeline_accessor.py
cytearc/datastore/pipeline_run.py
cytearc/datastore/plot_accessor.py
cytearc/datastore/summary.py
cytearc/datastore/_operations/__init__.py
cytearc/datastore/_operations/clustering.py
cytearc/datastore/_operations/embeddings.py
cytearc/datastore/_operations/enrichment_store.py
cytearc/datastore/_operations/features.py
cytearc/datastore/_operations/graph.py
cytearc/datastore/_operations/integration_metrics.py
cytearc/datastore/_operations/mapping.py
cytearc/datastore/_operations/mapping_reference.py
cytearc/datastore/_operations/paris_persistence.py
cytearc/datastore/_operations/presentation.py
cytearc/datastore/_operations/quality_control.py
cytearc/datastore/_operations/statistical_store.py
cytearc/datastore/_operations/trajectory.py
cytearc/embeddings/__init__.py
cytearc/embeddings/imported.py
cytearc/embeddings/imported_storage.py
cytearc/embeddings/initialization.py
cytearc/embeddings/reduction.py
cytearc/embeddings/sgtsne.py
cytearc/embeddings/umap.py
cytearc/embeddings/harmony/__init__.py
cytearc/embeddings/harmony/api.py
cytearc/embeddings/harmony/models.py
cytearc/embeddings/harmony/optimizer.py
cytearc/features/__init__.py
cytearc/features/aggregation.py
cytearc/features/gene_families.py
cytearc/features/gene_reference.py
cytearc/features/identity.py
cytearc/features/scoring.py
cytearc/features/statistical.py
cytearc/features/values.py
cytearc/features/variability.py
cytearc/features/enrichment/__init__.py
cytearc/features/enrichment/aucell.py
cytearc/features/enrichment/net.py
cytearc/features/enrichment/results.py
cytearc/features/enrichment/waggr.py
cytearc/features/genomic/__init__.py
cytearc/features/genomic/intervals.py
cytearc/features/genomic/melding.py
cytearc/features/markers/__init__.py
cytearc/features/markers/rank.py
cytearc/features/markers/regression.py
cytearc/features/markers/search.py
cytearc/features/markers/table.py
cytearc/graph/__init__.py
cytearc/graph/arguments.py
cytearc/graph/distances.py
cytearc/graph/feature_projection.py
cytearc/graph/kinds.py
cytearc/mapping/__init__.py
cytearc/mapping/artifact.py
cytearc/mapping/confidence.py
cytearc/mapping/features.py
cytearc/mapping/label_transfer.py
cytearc/mapping/models.py
cytearc/mapping/projection.py
cytearc/mapping/reference.py
cytearc/mapping/symphony.py
cytearc/matrix/__init__.py
cytearc/matrix/_indexing.py
cytearc/matrix/_operations.py
cytearc/matrix/_reductions.py
cytearc/matrix/chunked.py
cytearc/merge/__init__.py
cytearc/merge/datasets.py
cytearc/merge/features.py
cytearc/merge/metadata.py
cytearc/merge/models.py
cytearc/merge/row_plan.py
cytearc/merge/writer.py
cytearc/metadata/__init__.py
cytearc/metadata/arguments.py
cytearc/metadata/artifacts.py
cytearc/metadata/encoding.py
cytearc/metadata/membership.py
cytearc/metadata/queries.py
cytearc/metadata/rows.py
cytearc/metadata/selection.py
cytearc/metadata/table.py
cytearc/metrics/__init__.py
cytearc/metrics/_rows.py
cytearc/metrics/_types.py
cytearc/metrics/association.py
cytearc/metrics/cluster_selection.py
cytearc/metrics/cluster_separability.py
cytearc/metrics/concordance.py
cytearc/metrics/connectivity.py
cytearc/metrics/graph.py
cytearc/metrics/lisi.py
cytearc/metrics/silhouette.py
cytearc/neighbors/__init__.py
cytearc/neighbors/diffusion.py
cytearc/neighbors/graph.py
cytearc/neighbors/index.py
cytearc/neighbors/integration.py
cytearc/neighbors/stages.py
cytearc/plotting/__init__.py
cytearc/plotting/_contracts.py
cytearc/plotting/_data.py
cytearc/plotting/_deps.py
cytearc/plotting/_display.py
cytearc/plotting/_figure.py
cytearc/plotting/_heatmap_utils.py
cytearc/plotting/_raster.py
cytearc/plotting/_style.py
cytearc/plotting/cluster_connectivity.py
cytearc/plotting/cluster_tree.py
cytearc/plotting/composition.py
cytearc/plotting/diagnostics.py
cytearc/plotting/distribution.py
cytearc/plotting/embedding.py
cytearc/plotting/embedding_raster.py
cytearc/plotting/heatmaps.py
cytearc/plotting/mapping.py
cytearc/plotting/modality_weights.py
cytearc/plotting/recipes.py
cytearc/plotting/summary.py
cytearc/quality_control/__init__.py
cytearc/quality_control/cell_cycle.py
cytearc/quality_control/cell_cycle_genes.py
cytearc/quality_control/doublets.py
cytearc/quality_control/filtering.py
cytearc/quality_control/hto.py
cytearc/readers/__init__.py
cytearc/readers/_assay_names.py
cytearc/readers/_h5ad_columns.py
cytearc/readers/_h5ad_inspect.py
cytearc/readers/_sparse.py
cytearc/readers/_text.py
cytearc/readers/cellranger.py
cytearc/readers/csv.py
cytearc/readers/h5ad.py
cytearc/readers/mtx.py
cytearc/readers/seurat.py
cytearc/readers/_rds/__init__.py
cytearc/readers/_rds/_lazy.py
cytearc/readers/_rds/_model.py
cytearc/readers/_rds/_parser.py
cytearc/readers/_rds/_storage.py
cytearc/readers/_rds/_types.py
cytearc/readers/_seurat/__init__.py
cytearc/readers/_seurat/bpcells.py
cytearc/readers/_seurat/errors.py
cytearc/readers/_seurat/factory.py
cytearc/readers/_seurat/fragments.py
cytearc/readers/_seurat/hdf5.py
cytearc/readers/_seurat/operations.py
cytearc/readers/_seurat/paths.py
cytearc/readers/_seurat/sources.py
cytearc/readers/_seurat/values.py
cytearc/storage/__init__.py
cytearc/storage/ann_index.py
cytearc/storage/arrays.py
cytearc/storage/artifact_writer.py
cytearc/storage/artifacts.py
cytearc/storage/async_execution.py
cytearc/storage/budget.py
cytearc/storage/copy.py
cytearc/storage/count_dtype.py
cytearc/storage/count_matrix.py
cytearc/storage/counts_t_contract.py
cytearc/storage/destinations.py
cytearc/storage/errors.py
cytearc/storage/execution.py
cytearc/storage/feature_selection.py
cytearc/storage/feature_stream.py
cytearc/storage/finite_values.py
cytearc/storage/geometry.py
cytearc/storage/identity.py
cytearc/storage/io_policy.py
cytearc/storage/layout.py
cytearc/storage/lineage.py
cytearc/storage/materialize.py
cytearc/storage/metadata_keys.py
cytearc/storage/operation_revisions.py
cytearc/storage/parallel.py
cytearc/storage/partition.py
cytearc/storage/pipeline_runs.py
cytearc/storage/profiles.py
cytearc/storage/refs.py
cytearc/storage/schema.py
cytearc/storage/selections.py
cytearc/storage/sharding.py
cytearc/storage/stores.py
cytearc/storage/types.py
cytearc/storage/validation_scope.py
cytearc/tools/__init__.py
cytearc/tools/repack_zarr.py
cytearc/trajectory/__init__.py
cytearc/trajectory/artifacts.py
cytearc/trajectory/fate.py
cytearc/trajectory/feature_dynamics.py
cytearc/trajectory/parameters.py
cytearc/trajectory/pseudotime.py
cytearc/trajectory/results.py
cytearc/utils/__init__.py
cytearc/utils/arguments.py
cytearc/utils/arrays.py
cytearc/utils/compute.py
cytearc/utils/count_values.py
cytearc/utils/digest.py
cytearc/utils/logging.py
cytearc/utils/moments.py
cytearc/utils/numba.py
cytearc/utils/process.py
cytearc/utils/progress.py
cytearc/utils/shutdown.py
cytearc/utils/strided.py
cytearc/utils/warnings.py
cytearc/writers/__init__.py
cytearc/writers/_materialize.py
cytearc/writers/_store.py
cytearc/writers/cellranger.py
cytearc/writers/counts_t.py
cytearc/writers/csv.py
cytearc/writers/export.py
cytearc/writers/h5ad.py
cytearc/writers/seurat.py
cytearc/writers/sparse.py
cytearc/writers/subset.py
skills/cytearc-single-cell/SKILL.md
skills/cytearc-single-cell/references/clustering-and-embedding.md
skills/cytearc-single-cell/references/data-access.md
skills/cytearc-single-cell/references/features-and-graphs.md
skills/cytearc-single-cell/references/gene-blacklists.md
skills/cytearc-single-cell/references/integration-and-comparisons.md
skills/cytearc-single-cell/references/markers-and-annotation.md
skills/cytearc-single-cell/references/performance-and-export.md
skills/cytearc-single-cell/references/pipeline-runs-and-artifacts.md
skills/cytearc-single-cell/references/plotting.md
skills/cytearc-single-cell/references/quality-control.md
skills/cytearc-single-cell/scripts/inspect_store.py