CytePool

Test which genes, cell types and pathways change between conditions in single-cell and bulk RNA-seq.

Cells from one donor are not independent replicates. CytePool pools each sample and cell type into a cube of pseudobulk profiles, and runs limma, edgeR, DESeq2, dream, variancePartition, propeller, fgsea, GSVA, decoupler, metafor and SumRank in Python on numpy arrays.

Install

Requires Python 3.13 or newer:

pip install cytepool

For AnnData, MuData and plotting, install pip install "cytepool[mudata,plot]". See Installation.

Example

Pool cells into a cube, then test a stimulation across cell types with limma-voom, pairing samples by donor:

from cytepool import Design, camera, from_cells, limma_voom, read_gmt

cube = from_cells(
    counts,  # cells x genes, e.g. adata.X
    sample_labels=cell_sample,  # e.g. adata.obs["sample"]
    group_labels=cell_type,  # e.g. adata.obs["cell_type"]
    samples=samples,  # sample_id, donor, condition
    features=genes,  # feature_id and symbol, or adata.var
)
design = Design(
    cube.samples,
    "~ donor + condition",
    levels={"condition": ["ctrl", "stim"]},
    contrasts={"stim_vs_ctrl": "conditionstim"},
)
result = limma_voom(cube, design)
table = result.table("Monocytes", "stim_vs_ctrl")  # topTable columns

# Test pathway response in monocytes from a GMT file.
hallmark = read_gmt("h.all.v2026.2.Hs.symbols.gmt")
pathways = camera(result, hallmark, group="Monocytes", id_column="symbol")

If you already pooled profiles in scanpy, decoupler or LIANA, import them with from_anndata or from_mudata. See the Quick start and Gene sets and pathways.

What CytePool answers

Choosing a method compares the alternatives for each question, and Validation benchmarks CytePool against the reference packages.

Documentation

The documentation is at https://docs.nygen.io/CytePool/.

Development

uv sync --extra test --group dev --group docs
uv run pytest
uv run ruff check cytepool tests validation docs
uv run ruff format --check cytepool tests validation docs
uv run mypy cytepool
make -C docs api

License

BSD 3-Clause. See LICENSE and THIRD_PARTY_NOTICES.md.