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

feat(qtl): ingest credible sets from single cell derived QTLs #630

Merged
merged 7 commits into from
Jun 6, 2024

Conversation

ireneisdoomed
Copy link
Contributor

@ireneisdoomed ireneisdoomed commented May 31, 2024

✨ Context

This PR closes opentargets/issues#3332

🛠 What does this PR implement

  • Changes in the study schema to represent the tissue or cell type from which the eQTL has been derived. I've renamed tissueId to biosampleId to represent this
  • Update of the table containing the study metadata
  • Minor updates in the configuration of the eQTL Catalogue input variables

🙈 Missing

🚦 Before submitting

  • Do these changes cover one single feature (one change at a time)?
  • Did you read the contributor guideline?
  • Did you make sure to update the documentation with your changes?
  • Did you make sure there is no commented out code in this PR?
  • Did you follow conventional commits standards in PR title and commit messages?
  • Did you make sure the branch is up-to-date with the dev branch?
  • Did you write any new necessary tests?
  • Did you make sure the changes pass local tests (make test)?
  • Did you make sure the changes pass pre-commit rules (e.g poetry run pre-commit run --all-files)?

@project-defiant
Copy link
Contributor

LGTM

@ireneisdoomed ireneisdoomed merged commit fd3154a into dev Jun 6, 2024
4 checks passed
@ireneisdoomed ireneisdoomed deleted the il-scqtl branch June 6, 2024 16:00
project-defiant pushed a commit that referenced this pull request Jun 14, 2024
* chore: prototype ingestion of sceqtls

* chore: use credible sets from ftp

* feat(study_index): rename tissuefromsourceid to biosamplefromsourceid to accommodate cell type ids

* chore: update output paths to final destination
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Incorporate scQTLs from Kaur
2 participants