2024-09-25 Community Announcement

[Jen-OMalley]

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

Reminder: If you are currently working on an analysis, please keep the below deadlines in mind! Although the final submission deadline is in November, we anticipate it will take at least one month between your initial pull request and the final submission acceptance required for grant eligibility.

• Final Table Submission Deadline: November 1, 2024 (5PM EDT)
• Application Submission Deadline, if eligible: November 15, 2024 (5PM EST) or within ten days of notification of eligibility, whichever is sooner

We are available if you’d like to discuss your analysis plans or have any questions about the contributing process!

What the Data Lab is working on

rOpenScPCA package: Ideas for functionality

Since our last update:

• @sjspielman worked on rOpenScPCA, an R package to house functions for general use across OpenScPCA modules!
  • We started by adding a function to perform clustering. View the proposed clustering utility module.
  • The package is being developed in the feature/rOpenScPCA branch.

Coming next:

• We will add functionality to evaluate clustering results.
• We plan to write an example notebook demonstrating how to use the package.

Explore computing metacells

Coming next:

• @jashapiro will add a notebook to look at the results of metacell analysis.

What community members are working on

• @maud-p has continued to make progress on the Wilms tumor dataset annotation (SCPCP000006). View the relevant issues and open pull request.
• @danhtruong is working on the DSRCT Dataset Analysis (SCPCP000013). Check out the relevant issue.
• @JingxuanChen7 is working on the Wilms Tumor annotation (SCPCP000014).
• @UTSouthwesternDSSR is working on the Non-early T-cell precursor T-cell acute lymphoblastic leukemia (non-ETP ALL) annotation (SCPCP000003). View the relevant issue and open pull request.
• @georginaalbadri has started Single-cell RNA sequencing of pediatric high-grade gliomas (SCPCP000001). Check out the relevant issue.

More analysis proposals from the community

Click the link in the Proposed analysis column to read the full discussion post. You can also view all current analysis ideas, and share your own ideas, in the Propose a new analysis category!

Group ID	Project ID	Diagnosis	Proposed analysis
SCPCAB0005	SCPCP000003	Early T-cell precursor T-cell acute lymphoblastic leukemia	#629
SCPCAB0009	SCPCP000004	Neuroblastoma	#589
SCPCAB0010	SCPCP000006	Wilms tumor	#603
SCPCAB0017	SCPCP000011	Retinoblastoma	#588
SCPCAB0019	SCPCP000013	Clear cell sarcoma, Clear cell sarcoma of the kidney, Embryonal sarcoma, Epithelioid sarcoma, Gastrointestinal stromal tumor, Infantile fibrosarcoma, Spindle sarcoma, Synovial sarcoma, Undifferentiated round cell sarcoma	#604
SCPCAB0024	SCPCP000017	Osteosarcoma	#601
SCPCAB0027	SCPCP000023	Osteosarcoma	#587

Reproducible Research Practices Workshop

Interested in attending a Data Lab workshop? Applications are open for our next Reproducible Research Practices workshop taking place on October 23-24 in Milwaukee, WI. Data Lab staff will introduce principles and techniques to achieve reproducible results in computational cancer research. We’ll show you the fundamentals of commonly used approaches in reproducibility that you can apply to increase the impact of your research by making your findings more robust and reliable!

Learn more, including how to apply, in our full blog post announcement! Travel reimbursement is available for qualifying participants. Applications will remain open until Friday, September 27. Please feel free to share this information with others who may be interested.

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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 [email protected], or send a message on our #open-scpca Slack channel.