2024-06-18 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 worked on validating tumor cell annotations by confirming high expression of EWS-FLI1 targets, the fusion gene present in Ewing sarcoma tumor cells.
  • To do this, we calculated gene set scores for commonly used EWS-FLI1 gene set signatures.

Next, we are:

• Continuing to validate and finalize the tumor cell annotations obtained from annotating each sample using marker genes and copy number variation methods.
  • This includes looking at the consensus between each of the CNV methods (CopyKAT, InferCNV), marker gene expression, and EWS-FLI1 gene set scores.
• We hope to validate a few samples and then use those samples as a reference to annotate all Ewing sarcoma samples on the ScPCA Portal.

Coming soon: Look out for a discussion post that will go over the current results of this analysis. We will also be seeking your feedback! This post will be shared in the Analysis category within the next couple of weeks.

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

#364 Doublet Detection

Currently, we are:

• Comparing performance of doublet detection methodologies across multiple benchmarking datasets.

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

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 are continuing to update the OpenScPCA documentation based on feedback we received through information architecture (IA) validation.
  • We are adding a new section in our documentation about ensuring reproducibility in analysis modules and across the OpenScPCA project.

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.