2024-07-16 Community Update

[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:

• We explored using a sample where we have already annotated tumor cells (SCPCS000490) as a reference to annotate additional samples using SingleR.
• We created a workflow that uses AUCell to annotate tumor cells for all samples in the project.

Next, we will:

• Evaluate the results from using AUCell and refine tumor cell annotations for any samples that did not perform well.
  • In particular, we plan to use SingleR with multiple reference samples to annotate the samples that did not work well with AUCell.

Read #292 for more details about this analysis including the scientific goals, planned methods and more.

#364 Doublet Detection

Since our last update:

• We identified scDblFinder as a tool we will use to apply doublet detection to all ScPCA samples.

Read #364 for more details about this analysis including the scientific goals, planned methods and more.

#362 Explore computing metacells

• We are creating a module to explore methods for computing metacell reductions of single-cell data.
• The full ScPCA dataset is quite large, and individual cell data can be noisy, making some inference difficult.
  • There have been a number of methods proposed to combine information across cells into "metacells".
  • Creating metacells reduces the dataset size and can be helpful when performing downstream analysis.
• We are starting with an exploration of SEACells and will evaluate this method for use with ScPCA data.

Read #362 for more details about this analysis including the scientific goals, planned methods and more.

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

Annotating cell types for existing datasets on the ScPCA Portal

We recently announced that grants are now available for eligible researchers who annotate cell types for all samples in a given group as identified by the sample table found here.

Community members are currently working on:

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	#587

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

• Read the full eligibility and acceptance criteria to determine if you meet the requirements
• Read this dicussion post to learn more about the available grants and how to get started

What the Data Lab is working on

• As part of the doublet-dection module, we identified scDblFinder as a doublet detection method we would like to run on all ScPCA samples. We plan to provide the results from running this analysis on all samples in the workflow results bucket on S3.
• In order to do this, we will be working on porting over the analysis from the doublet-detection module to the OpenScPCA-nf workflow. Once this is complete, the results will be available for everyone to access and use in their own analysis.

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 scpca@ccdatalab.org, or send a message on our #open-scpca Slack channel.