2024-11-19 Community Announcement

[Jen-OMalley]

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

General Announcement

Out of office

• The Data Lab will be out of the office next Thursday, November 28 and Friday, November 29 in observance of Thanksgiving.

What the Data Lab is working on

rOpenScPCA package: Ideas for functionality

Since our last update:

• @sjspielman created a separate repository containing the rOpenScPCA package, which offers utility functions to support single-cell RNA-Seq analysis in the OpenScPCA project. With the new repository, it will be easier for others to install the package!

Coming next:

• In ScPCA, we use Ensembl IDs as the primary identifier. But some users prefer to use gene symbols for interpretability. @jashapiro is working on adding a set of functions to rOpenScPCA that will convert Ensembl IDs to gene symbols.
• @jashapiro is also adding a function that converts ScPCA-formatted SingleCellExperiment objects to Seurat objects. This will include conversion of metadata to Seurat default locations as appropriate, as well as optional conversion of the gene IDs to gene symbols.

Annotate cell types in Ewing sarcoma samples on the Portal

• @allyhawkins will resume this analysis! We will start by updating the current clustering report to utilize some of the new functions from the rOpenScPCA package.

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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 [email protected], or send a message on our #open-scpca Slack channel.