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

Fix cell cycle score for CELLxGENE census data #338

Closed
wants to merge 5 commits into from

Conversation

mumichae
Copy link
Collaborator

@mumichae mumichae commented Jan 17, 2024

Describe your changes

  • Use 'feature_names' for cell cycle scores to ensure that gene symbols are passed instead of Ensembl IDs.
  • Ensure 'feature_names' are present in the data during the dataset processing step.
  • Add test resource scripts for CELLxGENE census data
  • Upload test resources to AWS
  • Extend testing script to allow for multiple test setups (only updating different input files for now)

Issue ticket number and link

Closes #331

Checklist before requesting a review

  • I have performed a self-review of my code

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Bug fixes
  • Proposed changes are described in the CHANGELOG.md

  • CI Tests succeed and look good!

@rcannood
Copy link
Member

Merged in #325.

@rcannood rcannood closed this Jan 27, 2024
@rcannood rcannood deleted the cell_cycle_genes branch February 7, 2024 14:39
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.

[bat_int] cell cycle genes not in adata for cellxgene_census dataset
2 participants