2025-07-29 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

Out of office

• The Data Lab team is holding a training workshop from August 4-8. We will be slower to respond during this time.

Are you interested in receiving a grant for your contributions to the OpenScPCA project?

• We're seeking pediatric cancer researchers at non-profit institutions with experience analyzing single-cell RNA-seq datasets to annotate and assign cell types to existing ScPCA datasets!
• Grants are offered in two categories: the Advisor Award and the Analyst Award, each with distinct submission requirements.
• Check out this announcement to view the full table of available grants, learn about eligibility requirements, and to get started!

What the Data Lab is working on

Cell type annotation

• Since last time:
  • We explored and validated results from running SingleR on all samples from SCPCP000004.
  • We began preparing to run label transfer with scANVI using NBAtlas as a reference to annotate samples from SCPCP000004.
• Coming next:
  • We will run scANVI with NBAtlas as a reference to annotate samples from SCPCP000004.

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.

---

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.