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Add exploratory notebook for SingleR results on NB samples #1172

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sjspielman opened this issue Jun 12, 2025 · 0 comments
Open

Add exploratory notebook for SingleR results on NB samples #1172

sjspielman opened this issue Jun 12, 2025 · 0 comments
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@sjspielman
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If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.

Part of #1151

Describe the goals of the changes to the analysis module.

The goal of this issue is to add an exploratory notebook to look at SingleR results from classifying NB samples using the NBAtlas reference. This notebook should contain at least:

  • The SingleR heatmap of assigned cell types
    • Maybe a delta median plot
  • A comparison between consensus cell types and SingleR cell types, using a heatmap colored by Jaccard similarity
  • A UMAP, because we must
  • Validation of SingleR cell types with marker genes

I'm frankly still back and forth for whether we're better served with a template notebook to look at results for individual samples, vs an overall notebook to look at all samples at once. I will want to look at one set of results first to help me make this decision, but I think in the end we may indeed want a small notebook to look at individual samples, and a larger notebook to perform more validation and comparison with consensus. Therefore additional comments will be added to this issue, and/or sub-issues may be broken out, to accomplish all this.

What will your pull request contain?

Notebook for exploring SingleR results

Will you require additional software beyond what is already in the analysis module?

No

Will you require different computational resources beyond what the analysis module already uses?

No

If known, when do you expect to file the pull request?

No response

@sjspielman sjspielman self-assigned this Jun 12, 2025
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