AlexsLemonade / AlexsLemonade/OpenScPCA-analysis
Attempt to identify tumor cells in those non-ETP samples without B cells (SCPCP000003)
- 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.
#630
### Describe the goals of the changes to the analysis module.
The idea is to choose the best annotated sample with B cells (`SPCL000703`) and merge it with one of the samples without B cells, and correct the batch effect with Harmony, attempting to deduce the tumor/normal status of those cells from sample without B cells by the clustering pattern, if there is any.
### What will your pull request contain?
scripts for merging/batch effect corrected object and showing the umap plots of object
### Will you require additional software beyond what is already in the analysis module?
Harmony
### Will you require different computational resources beyond what the analysis module already uses?
_No response_
### If known, when do you expect to file the pull request?
~Today or tomorrow
Contributor guide
Research direction
Start by reviewing Discussion #630 and the analysis module's existing workflows. The issue names sample SPCL000703 and the samples without B cells, and asks for scripts that merge and Harmony-correct the objects and show UMAP plots. Done means producing those scripts and plots, with the tumor/normal inference documented if clustering supports it.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100