AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Explore cells that are classified as both immune and tumor in Ewing samples

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#1,087 0 comments 0 reactions 1 assignee Claimed by @allyhawkins View on GitHub
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Description

### If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.

#696

### Describe the goals of the changes to the analysis module.

In https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1084, it was noted that there are a small handful of cells across 3 samples that are classified as either macrophage or T cell by the consensus cell types and as tumor cells using expression of marker genes. We might consider taking a closer look at these cells and see why they are being classified as both.

### What will your pull request contain?

An exploratory notebook that looks at the expression of normal markers (either macrophage or T cell) in compared to tumor marker gene expression. This should help us identify which label is more appropriate.

### 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_

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