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Backport PR #3844 on branch 1.11.x (docs: fix score_genes citation) #3850

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Oct 28, 2025
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Backport PR #3844 on branch 1.11.x (docs: fix score_genes citation) #3850

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11 changes: 11 additions & 0 deletions docs/references.bib
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Original file line number Diff line number Diff line change
Expand Up @@ -869,6 +869,17 @@ @article{Tarashansky2019
month = {sep},
}

@article{Tirosh2016,
author = {Tirosh, Itay and Izar, Benjamin and Prakadan, Sanjay M and Wadsworth, Marc H and Treacy, Daniel and Trombetta, John J and Rotem, Asaf and Rodman, Christopher and Lian, Christine and Murphy, George and others},
title = {Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq},
journal = {Science},
volume = {352},
number = {6282},
pages = {189--196},
year = {2016},
publisher = {American Association for the Advancement of Science},
}

@misc{Traag2017,
author = {Traag, Vincent},
doi = {10.5281/ZENODO.35117},
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5 changes: 3 additions & 2 deletions src/scanpy/tools/_score_genes.py
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Expand Up @@ -69,13 +69,14 @@ def score_genes( # noqa: PLR0913
use_raw: bool | None = None,
layer: str | None = None,
) -> AnnData | None:
"""Score a set of genes :cite:p:`Satija2015`.
"""Score a set of genes :cite:p:`Tirosh2016`.

The score is the average expression of a set of genes after subtraction by
the average expression of a reference set of genes. The reference set is
randomly sampled from the `gene_pool` for each binned expression value.

This reproduces the approach in Seurat :cite:p:`Satija2015` and has been implemented
This reproduces the approach in Seurat :cite:p:`Tirosh2016` ("MITF and AXL expression
programs and cell scores" in materials and methods) and has been implemented
for Scanpy by Davide Cittaro.

Parameters
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