AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Add script to prepare references for use

Open
#1,413 1 comment 0 reactions 1 assignee Claimed by @allyhawkins View on GitHub
analysis
Dominant language
HTML
Stars
16
Forks
24
Avg merge
3d 5h
Merged PRs (30d)
4

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.

The first step in annotating samples with OsteoCAR is to get OsteoCAR ready for use. We'll need to get SCE & AnnData objects of the Seurat files from the atlas we'll need.

Code will have similarities to this script we used to prepare the NBAtlas reference: https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/main/analyses/cell-type-neuroblastoma-04/scripts/00_convert-nbatlas.R

### What will your pull request contain?

- module analysis run script
- script to prepare the osteocar references
- associated environment updates

### 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_

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.