API Reference

sc_tools follows the scanpy API pattern. Import the package as import sc_tools as st and access modules via st.pp, st.pl, st.tl, st.qc, st.memory, st.utils.

Module overview

Module	Description
sc_tools.pp — Preprocessing	Preprocessing — normalization, batch integration, dimensionality reduction, clustering.
sc_tools.pl — Plotting	Plotting — spatial plots, heatmaps, QC plots, enrichment dot plots.
sc_tools.tl — Analysis Tools	Tools — signature scoring, gene set loading, ORA/GSEA, deconvolution, colocalization.
sc_tools.qc — Quality Control	Quality control — QC metrics, spot filtering, sample classification, HTML reports.
sc_tools.ingest — Data Ingestion	Ingestion — batch manifests, modality loaders (Visium/HD/Xenium/IMC), SLURM helpers.
sc_tools.validate — Checkpoint Validation	Validation — checkpoint metadata contracts (Architecture.md Section 2.2).
sc_tools.pipeline — Phase DAG	Pipeline DAG — phase specs, dependency graph, available-next queries.
sc_tools.bm — Benchmarking	Benchmarking — integration comparison, segmentation quality metrics.
sc_tools.storage — Storage Abstraction	Storage — fsspec URI abstraction for local, S3, SFTP, GCS, Azure, Box.
sc_tools.registry — Project Registry	Registry — SQLAlchemy project/dataset/job tracking (SQLite or PostgreSQL).
sc_tools.memory — GPU and Memory	Memory / GPU — GPU detection, memory profiling, aggressive cleanup.
sc_tools.utils — Utilities	Utilities — signature helpers, versioned save paths.