2024-12-03 Community Announcement

[Jen-OMalley]

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

General Announcements

Out of office

• The Data Lab is holding a training workshop from December 10-12, 2024. Most of the team will be out of the office and slower to respond during that time.

What the Data Lab is working on

rOpenScPCA package: Ideas for functionality

Since our last update:

• @jashapiro added a set of functions to rOpenScPCA that will convert Ensembl IDs to gene symbols.

Coming next:

• @jashapiro is 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

Since last time:

• @allyhawkins updated the clustering workflow to utilize some of the new functions from the rOpenScPCA package.

Coming next:

• We will run the clustering workflow on all samples in SCPCP000015 and the reports will be saved to the results directory.
• We will then create a template report used to look at cell types and marker gene sets in the assigned clusters. This report will be rendered for each sample using the optimal clustering parameters determined by looking at the output from the clustering workflow.

Find consensus of SingleR and CellAssign cell type labels

• The processed data available as part of our data releases includes the cell type annotation results from two reference-based, automated methods: SingleR and CellAssign. We aim to identify consensus cell type labels between the two methods.
  • First, we need to assign cell ontology identifiers to cell types in our CellAssign reference. @allyhawkins will start by updating our PanglaoDB reference to include a column with cell ontology IDs.
  • We will also create an exploratory notebook to find ontology-based rules for assigning a consensus cell type label with ScPCA samples.

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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.