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

scBulkDE

Contents