2024-05-22 Community Update

[Jen-OMalley]

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

Analysis in-progress

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

Since our last update:

• We explored methods for estimating copy number variations in Ewing sarcoma samples and compared them to annotations using tumor marker genes. This included InferCNV, CopyKAT, and SCEVAN.

In the coming weeks:

• We will create a small workflow that can be used to annotate tumor cells in a single sample using both marker genes and CNV inference.
• We will run this workflow on additional samples and evaluate the results, which will help us narrow down the methods we'll use for annotating tumor cells.

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

Analysis we expect to start

#364 Doublet detection

• In scpca-nf, the data processing pipeline behind the ScPCA Portal, we do not currently do any analysis or flagging of doublet cells. Adding flagging of potential doublets could improve data quality for cell typing and many other analyses.

In the coming weeks:

• We are beginning to explore performance of doublet detection methodologies and their potential use on ScPCA data.

Read #364 for more details about 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

Workflow updates:

• We recently shared that as part of the OpenScPCA-nf workflow, we are adding the merged workflow from scpca-nf to generate merged objects.
  • Merged objects are available on the Portal now, but with the addition of the workflow, they will be available in the OpenScPCA-nf workflow results bucket.
• A script will be available to download any results from the OpenScPCA-nf workflow, including merged objects, for contributors to 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.