Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

SysVI tutorial #212

Open
wants to merge 22 commits into
base: main
Choose a base branch
from
Open

SysVI tutorial #212

wants to merge 22 commits into from

Conversation

Hrovatin
Copy link

Associated with scverse/scvi-tools#2383

Formatting

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

Reproducibility

  • My tutorial works on Google Colab
    Could you help with this?
  • [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

  • [x ] Counts and normalized data should co-exist in the datasets, see the API overview for an example
  • [ x] For scRNA-seq data, normalization should be counts per median library size and then log1p transformed -- if not, a reason should be given
    Data is normalized to fixed number of total counts as it was normalized separately for mouse and human. If median library size was used for normalization the two datasets would not be comparable.

Copy link

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.


Powered by ReviewNB

Copy link
Contributor

@martinkim0 martinkim0 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I'm approving this for now, but this needs to be run again once scverse/scvi-tools#2421 is merged into main since we require that tutorials are run top to bottom in a container.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

2 participants