2024-07-31 Community Announcement

[Jen-OMalley]

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

Analyses in-progress

#292 Annotate cell types in Ewing sarcoma samples on the Portal

Since our last update:

• @allyhawkins evaluated the results from annotating tumor cells with AUCell.
• We used SingleR to further define tumor cell and normal cell populations.

Next:

• @allyhawkins will refine the assignments from SingleR by clustering the cells.
• Then, we’ll validate that:
  • clusters with tumor cells have higher expression of tumor marker genes.
  • clusters with normal cells express genes specific to that normal cell population.

#362 Explore computing metacells

Since our last update:

• @jashapiro started a module to explore using metacell methods to create reduced data sets.
• We began with an exploration of SEACells to evaluate this method for use with ScPCA data.

Next:

• @jashapiro will create an exploratory analysis notebook for SEACells to see how well this method is performing on ScPCA datasets. The goal is to allow comparisons among different metacell methods.
• The notebook will include:
  • Calculating statistics such as compactness and separation to look at how well the metacells cover the original cell types.
  • A visualization of the metacells overlaid on the original cells in a UMAP.
  • A summary of computational requirements that were required for calculating the metacells.

Analyses we expect to start this sprint

#635 Wilms tumor dataset annotation

• @maud-p is the first community member, outside of the Data Lab, to file a pull request! 🎉
• See Wilms Tumor Dataset Annotation (SCPCP000006) #635 for more details about their scientific goals and planned methods for annotating the Wilms tumor samples in the SCPCP000006 dataset.

View all current analysis ideas, and share your own ideas, in the Propose a new analysis category!

What the Data Lab is working on

• We have completed the first versioned release of OpenScPCA-nf, with results that include doublet detection. We are working on making these results available as soon as possible!

What community members are working on

Group ID	Project ID	Diagnosis	Proposed analysis
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.