2024-12-17 Community Announcement

[Jen-OMalley]

2024-12-17 sprint announcement

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 will be out of the office from December 25, 2024 to January 1, 2025.

What the Data Lab is working on

rOpenScPCA package: Ideas for functionality

Since last time:

• @sjspielman will resume building the hello-clusters module, which includes adding example notebooks.
  • We're working on notebooks to demonstrate clustering with rOpenScPCA and sweeping cluster parameters with rOpenScPCA.

Annotate cell types in Ewing sarcoma samples on the Portal

Since last time:

• @allyhawkins updated part of the clustering workflow to compare clustering results to cell types and marker gene sets. This report is generated after the initial clustering evaluation.

Coming next:

• @allyhawkins is planning to annotate tumor cell states for all Ewing sarcoma tumor cells. We will start by creating marker gene lists for expected cell states.
• Then we will create a notebook to explore identifying tumor cell states in Ewing samples using these marker gene lists.

Seurat conversion

• @jashapiro added a function that converts ScPCA-formatted SingleCellExperiment objects to Seurat objects.
  • This includes conversion of metadata to Seurat default locations as appropriate, as well as optional conversion of the gene IDs to gene symbols.
  • We will add modules to the rOpenScPCA and OpenScPCA-nf repositories with the ultimate goal of producing processed Seurat objects for contributors’ use.

Find consensus of SingleR and CellAssign cell type labels

Since last time:

• @allyhawkins assigned cell ontology identifiers to cell types in our CellAssign reference. We started by updating our PanglaoDB reference to include a column with cell ontology IDs.

Coming next:

• @allyhawkins is creating an exploratory notebook to find ontology-based rules for assigning a consensus cell type label with ScPCA samples.
• We will then create a reference table with all possible combinations of cell type labels between the SingleR reference (Blueprint Encode Data) and CellAssign reference (PanglaoDB) and an appropriately assigned consensus label.

What the community is working on

• @cansavvy will be adding new functionality to the rOpenScPCA package.
  • This includes a function for generating stats for clustering results and a function for plotting clustering metrics across multiple clustering results.

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