I have always had a question: do I need to scale my adata before running sc.tl.score_genes? - Githubissues

scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.

https://scanpy.readthedocs.io

BSD 3-Clause "New" or "Revised" License

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I have always had a question: do I need to scale my adata before running sc.tl.score_genes? #3080

Closed christophechu closed 4 months ago

christophechu commented 4 months ago

Please make sure these conditions are met

[X] I have checked that this issue has not already been reported.
[X] I have confirmed this bug exists on the latest version of scanpy.
[X] (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

I have always had a question: do I need to scale my adata before running sc.tl.score_genes?

Minimal code sample

sc.tl.score_genes_cell_cycle(adata_hvg, layers='scaled', s_genes=s_genes, g2m_genes=g2m_genes)

Error output

No response

Versions

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flying-sheep commented 4 months ago

Hi, this issue tracker is better suited for bugs or enhancement request. Please ask e.g. here: https://discourse.scverse.org/