2025-10-07 Community Announcement

[Jen-OMalley]

Hello everyone. Here are the latest OpenScPCA updates! Please feel free to reply here with any questions or comments.

General announcement

Grant deadlines

Reminder: Please keep the deadlines below in mind if you are working on an analysis or protocol associated with a grant opportunity. If you intend to contribute further, we encourage you to do so this week to avoid missing any deadlines.

• Analyst Awards: The final table and Description section of the README must be approved via pull request by 5 PM Eastern Daylight Time on October 31, 2025.
• Advisor Awards: The final protocol must be approved, as indicated by a GitHub Discussions comment from an ALSF Childhood Cancer Data Lab staff member, by 5 PM Eastern Daylight Time on October 31, 2025.
• Application Submission Deadline, if eligible: 5 PM Eastern Daylight Time on November 14, 2025 or within ten days of notification of eligibility, whichever is sooner.

What the Data Lab is working on

Cell type annotation

New cell type annotations are available in the workflow results bucket! Find more details in this announcement.

What the community is working on

• @cansavvy continues to work on adding new functionality to the rOpenScPCA package.
• @ShashTrip1 has submitted proposals for two groups of samples!
  • They have submitted plans to develop a detailed protocol for cell type annotation for a group of samples (SCPCAB0003). Read the full discussion post.
  • They plan to annotate cell types for another group of samples (SCPCAB0001). Read the full discussion post.
• @rs25-code has started annotating cell types for a group of samples (SCPCAB0027). Read the full discussion post.
• @parashardhapola has submitted plans to develop a protocol for LLM-driven cell type annotation for all samples on the ScPCA Portal. Read the full discussion post.
• @khoidnutsw plans to annotate cell types for a group of osteosarcoma samples (SCPCP000017). Read the full discussion post.
• @ermismd plans to annotate cell types for a group of osteosarcoma samples (SCPCP000018). Read the full discussion post.
• @eveegardner submitted a proposal to annotate cell types for a group of ETP ALL samples (SCPCAB0007). Read the full discussion post.

---

Do you need assistance getting set up, have an idea for an analysis that you are unsure about, or just have questions about where to begin with OpenScPCA? We can help! We are happy to provide guidance for getting started and we can even meet one-on-one to chat. Post in the Questions category, email us at scpca@ccdatalab.org, or send a message on our #open-scpca Slack channel.