2024-10-08 Community Announcement

[Jen-OMalley]

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

General Announcements

Out of office: Children's Brain Tumor Network (CBTN) Summit

Several science team members will attend the CBTN Summit on October 9-10.

• We will be slower to respond while we are out of the office.
• We'll be presenting the OpenScPCA project during poster sessions. Come say hello if you're there! 👋

Grant deadlines

Reminder: Please keep the below deadlines in mind if you are working on an analysis associated with a grant opportunity. The final submission deadline is less than one month away!

• 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

What the Data Lab is working on

rOpenScPCA package: Ideas for functionality

Since our last update:

• @sjspielman added a function to evaluate clustering results!

Coming next:

• We plan to write an example module demonstrating how to use the rOpenScPCA package. The goal is to provide a consistent approach to clustering that also allows convenient calculation of quality metrics across groups of clustering results to help users decide which set of clusters they might want to proceed with.

Explore computing metacells

Coming next:

• @jashapiro will continue working on 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 Wilm’s 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 and open pull request.
• @JingxuanChen7 is working on the Wilms Tumor annotation (SCPCP000014). View the relevant issue.
• @UTSouthwesternDSSR is working on the Non-early T-cell precursor T-cell acute lymphoblastic leukemia (non-ETP ALL) annotation (SCPCP000003). View the relevant issue.
• @UTSouthwesternDSSR has also started the Early T-cell precursor T-cell acute lymphoblastic leukemia (ETP ALL) annotation (SCPCP000003).
• @georginaalbadri is making progress on 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
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

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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.