sc_tools

sc_tools is a reusable Python toolkit for spatial and single-cell multiomics analysis. It follows the scanpy API pattern (sc_tools.pp, sc_tools.pl, sc_tools.tl, sc_tools.qc) and covers the full pipeline from raw data ingestion through downstream biology.

import sc_tools as st
import anndata as ad

# Load preprocessed AnnData (Phase 3 checkpoint)
adata = ad.read_h5ad("results/adata.normalized.p3.h5ad")

# Score gene signatures (Phase 3.5b)
signatures = st.tl.merge_gene_signatures(
    project_sigs, st.tl.load_hallmark()
)
st.tl.score_signature(adata, signatures)

# Spatial visualization
st.pl.multipage_spatial_pdf(adata, keys=["Hallmark/HYPOXIA"], output="figures/spatial.pdf")

Where to start

New to sc_tools? Start with the Installation guide, then follow the Tutorials.

Installation

Get sc_tools installed with the right optional extras for your workflow.

Installation

Tutorials

Step-by-step notebooks covering each pipeline phase with synthetic data.

Tutorials

API Reference

Complete function reference organized by module (pp, pl, tl, qc, memory, utils).

API Reference