2024-08-27 Community Announcement

[sjspielman]

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

Data Lab announcements

AACR Peds

We'll be presenting the OpenScPCA project during Poster Session B (poster #B075) at the AACR Advances in Pediatric Cancer Research Conference in Toronto next week.

Come say hi if you're there! 👋

Out of Office

• Data Lab team members will be out of the office on Monday, Sept 2nd, in observance of Labor Day.
• Several science team members will attend the AACR Peds conference on Thursday, Sept 5th, and Friday, September 6th.

We will be slower to respond when we are out of the office. We will do our best to reply to any questions, comments, and messages as soon as possible.

What the Data Lab is working on

• Last week, we created a new data release version (Data release: 2024-08-22 #723) with the id 2024-08-22.
  It is now available for download with the download-data.py script!
• Over the next week, we will be reaching out to OpenScPCA contributors to check in about the status of their analysis module development and offer help where we can.

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.