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Backport PR #3844 on branch 1.11.x (docs: fix score_genes citation) (#3850)
Co-authored-by: MLubetzki <[email protected]>
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docs/references.bib

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@@ -869,6 +869,17 @@ @article{Tarashansky2019
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month = {sep},
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}
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@article{Tirosh2016,
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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},
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title = {Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq},
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journal = {Science},
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volume = {352},
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number = {6282},
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pages = {189--196},
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year = {2016},
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publisher = {American Association for the Advancement of Science},
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}
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@misc{Traag2017,
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author = {Traag, Vincent},
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doi = {10.5281/ZENODO.35117},

src/scanpy/tools/_score_genes.py

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@@ -69,13 +69,14 @@ def score_genes( # noqa: PLR0913
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use_raw: bool | None = None,
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layer: str | None = None,
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) -> AnnData | None:
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"""Score a set of genes :cite:p:`Satija2015`.
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"""Score a set of genes :cite:p:`Tirosh2016`.
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The score is the average expression of a set of genes after subtraction by
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the average expression of a reference set of genes. The reference set is
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randomly sampled from the `gene_pool` for each binned expression value.
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This reproduces the approach in Seurat :cite:p:`Satija2015` and has been implemented
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This reproduces the approach in Seurat :cite:p:`Tirosh2016` ("MITF and AXL expression
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programs and cell scores" in materials and methods) and has been implemented
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for Scanpy by Davide Cittaro.
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Parameters

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