MrVI Quick Start Tutorial

scverse / scvi-tutorials

Notebooks used in scvi-tools tutorials

https://docs.scvi-tools.org/en/stable/tutorials/index.html

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

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MrVI Quick Start Tutorial #278

Closed justjhong closed 7 months ago

justjhong commented 7 months ago

Formatting

[x] My tutorial has only one top-level (#) header

Reproducibility

[x] My tutorial works on Google Colab
[x] My tutorial sets scvi.settings.seed = 0 at the beginning of the notebook
[x] 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

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canergen commented 7 months ago

Does the missing Colab check mean that it doesn't work or that it's not tested yet? In the first case can we make it pass? IMO it's the easiest way for reviewers to check algorithms and for users to get to know them.

martinkim0 commented 7 months ago

While you're at it, would you mind updating https://github.com/scverse/scvi-tutorials/blob/main/.github/workflows/run_linux_cuda.yml and https://github.com/scverse/scvi-tutorials/blob/main/.github/workflows/run_linux_cuda_branch.yml to include the new file? Thanks