scBulkDE

scBulkDE performs differential expression testing on pseudobulked single-cell data. It aggregates cells into pseudobulk samples, infers a full-rank design matrix and performs differential gene expression analysis while accounting for categorical and continuous covariates. Currently PyDeseq2 and ANOVA backends are supported for DE testing.

Key features

• Pseudobulk aggregation with quality control
• Covariate-aware design — categorical and continuous covariates with automated resolution of confounding factors
• Multiple DE engines — ANOVA F-test and PyDESeq2
• Fallback strategies — pseudoreplicate generation or single-cell testing when biological replicates are insufficient
• Scanpy drop-in — tl.rank_genes_groups stores results in adata.uns for seamless integration with scanpy.

Installation

You need to have Python 3.11 or newer installed on your system.

Install from PyPI:

pip install scbulkde

Or install the latest development version:

pip install git+https://github.com/quadbio/scBulkDE.git@main

Quick start

import scbulkde as scb

# One-step: pseudobulk + DE
de_result = scb.tl.de(
    adata,
    group_key="cell_type",
    query="B cells",
    reference="rest",
    replicate_key="donor",
    engine="anova",
)

de_result.results.head()

Or separate pseudobulking from testing for more control:

# Step 1 — Pseudobulk
pb_result = scb.pp.pseudobulk(
    adata,
    group_key="cell_type",
    query="B cells",
    reference="rest",
    replicate_key="donor",
)

# Step 2 — DE
de_result = scb.tl.de(pb_result, engine="anova")

Scanpy drop-in replacement

import scanpy as sc
import scbulkde as scb

scb.tl.rank_genes_groups(
    adata,
    groupby="cell_type",
    de_kwargs=dict(replicate_key="donor", engine="anova"),
)

sc.pl.rank_genes_groups(adata, n_genes=20)

Documentation

Please refer to the documentation, in particular the API documentation.

Release notes

See the changelog.

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Citation

t.b.a