2024-09-10 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

• @sjspielman is working on rOpenScPCA, an R package to house functions for general use across OpenScPCA modules! Read the full discussion post.
  • We will start by adding a function to perform clustering. View the proposed clustering utility module.

What community members are working on

Wilms tumor dataset annotation

• @maud-p has continued to make progress on this analysis!
  • Read the full discussion post for more details about the scientific goals and planned methods for annotating the Wilms tumor samples in the SCPCP000006 dataset.
  • Check out the relevant issues and open pull requests.

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
SCPCAB0001	SCPCP000001	Glioblastoma	#722
SCPCAB0005	SCPCP000003	Early T-cell precursor T-cell acute lymphoblastic leukemia	#629
SCPCAB0006	SCPCP000003	Non-early T-cell precursor T-cell acute lymphoblastic leukemia	#630
SCPCAB0009	SCPCP000004	Neuroblastoma	#589
SCPCAB0010	SCPCP000006	Wilms tumor	#603; #635
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
SCPCAB0020	SCPCP000013	Desmoplastic small round cell tumor	#583
SCPCAB0022	SCPCP000014	Wilms tumor	#628
SCPCAB0024	SCPCP000017	Osteosarcoma	#601
SCPCAB0027	SCPCP000023	Osteosarcoma	#587

Are you interested in obtaining a grant for annotating a group of samples?

• Grants are available for eligible researchers who annotate cell types for all samples in a given group as identified by this sample table.
• Read this discussion post to learn more about the available grants and how to get started.
• Read the full eligibility and acceptance criteria to determine if you meet the requirements

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.