2025-09-09 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

Are you attending the AACR Special Conference: Discovery and Innovation in Pediatric Cancer?

The Data Lab will be there to present our development of a reproducible workflow for an ongoing collaboration to identify therapeutic vulnerabilities in Ewing sarcoma.

If you're attending, visit our poster!

• "ews-nf: A custom workflow for tumor cell annotation and analysis of single-cell RNA-sequencing of paired patient Ewing sarcoma specimens from the Sean Karl cohort"
• Poster Session A, September 25 (7-9:30 PM)

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!

Grant deadlines

Reminder: Please keep the below deadlines in mind if you are working on an analysis or a protocol associated with a grant opportunity.

• 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

• Since last time:

  • @sjspielman ported the code used to annotate Neuroblastoma cell types to OpenScPCA-nf.
    Final annotations will be made available in the workflow results bucket.
  • We added a new module, cell-type-scimilarity, to OpenScPCA-nf to run SCimilarity on all samples. After generating the annotations, we created a short notebook summarizing results.
  • The cell-type-consensus module was updated to incorporate annotations from SCimilarity so that a consensus cell type will be assigned if two of three cell type annotation methods agree (SingleR, CellAssign, and SCimilarity).

• Coming next:

  • The cell-type-consensus module in OpenScPCA-nf will be updated to incorporate SCimilarity results and updated consensus cell types will be made available in the workflow results bucket. (Keep an eye out for a separate announcement about this!)
  • We will compare the new consensus cell types that incorporate cell type assignments from SCimilarity, SingleR, and CellAssign to the previous version of consensus cell types, which only considered assignments from SingleR and CellAssign.

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.

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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.