AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Add script to train SingleR model

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#1,414 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.

#1410

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

This issue tracks adding a script to train a SingleR model from a given osteocar reference file. We'll have a few references, but the script should call one at a time from the analysis module's run bash script.

Code will be similar to this from NBAtlas prep: https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/main/analyses/cell-type-neuroblastoma-04/scripts/01_train-singler-model.R

### What will your pull request contain?

- script to train singler
- run script from module bash script
- environment updates where needed

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

Presumably this is when SingleR gets added to renv

### 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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