Cannot find tutorial for regressing out cell cycle genes

[ntanmayee]

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.

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Hello, I am trying to find the tutorial to regress out cell cycle genes, and all the links in the documentation are broken.

1. The documentation for scanpy.tl.score_genes_cell_cycle has a link to an example, which is broken
2. The tutorials page in the documentation has another link which is also broken

Is this intentional? Could someone please help?

Thanks in advance!

[naity2]

I have the same question. Would someone from the development team help take a look at this issue? Thanks!

[davidmckinnon]

See here: https://nbviewer.org/github/theislab/scanpy_usage/blob/master/180209_cell_cycle/cell_cycle.ipynb

[Zethson]

Thank you @davidmckinnon !

[Zethson]

Actually, reopening this to ensure that we fix the broken links.

[ivirshup]

@Zethson, do you think we should move those to scverse?

[Zethson]

@Zethson, do you think we should move those to scverse?

Do you mean to this page? https://scverse.org/learn/

Or generally all of them? We might require stronger filtering options then because with all tools combined we would have a lot of vignettes.

Edit oh wait: I had no idea that we had this scanpy_usage repository. My answer is yes.

[ivirshup]

Oops, missed this.

Just moved. Should fix this issue.

[divyanshusrivastava]

(Minor) bug detected in the notebook shared above by @davidmckinnon
The notebook performs sc.pp.scale followed by sc.pp.score_genes_cell_cycle with default parameters.

In the default setting, sc.pp.score_genes_cell_cycle will take up the .raw layer of the anndata, if it exists. To be sure the scoring is performed on scaled counts, it should be done as

sc.tl.score_genes_cell_cycle(adata, s_genes=s_genes, g2m_genes=g2m_genes, use_raw=False)