MethylVI batch effect tutorial

[ethanweinberger]

Tutorial accompanies scverse/scvi-tools#2834

Formatting

• My tutorial has only one top-level (#) header

Reproducibility

• My tutorial works on Google Colab
• My tutorial sets scvi.settings.seed = 0 at the beginning of the notebook
• My tutorial has been run and includes outputs (e.g. plots, tables)

Other

• Counts and normalized data should co-exist in the datasets, see the API overview for an example
• For scRNA-seq data, normalization should be counts per median library size and then log1p transformed -- if not, a reason should be given (Note: not applicable to this tutorial as we're not using scRNA-seq)

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[canergen]

See comments overall looks fine. @ori-kron-wis can you help make the style consistent with other tutorials (I assume removing notebook style commands). These might change rendering on the webpage, which can end up ugly.

[ori-kron-wis]

@canergen not so sure what is the problem/difference in style? care to give a few examples?
I could think about adding a save/load model part and also make a new line for each input parameter in a scanpy function (this is to be equivalent to other tutorials)

[ethanweinberger]

Hi @canergen. Just wanted to check in to see if you had updates re: my and @ori-kron-wis's previous comments.

[canergen]

Please replace wget with pooch.

[canergen]

@ori-kron-wis Please merge after adding pooch.