AlexsLemonade / AlexsLemonade/OpenScPCA-analysis
Modify/explore clustering for Wilms tumor annotation (SCPCP000014)
- 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.
https://github.com/AlexsLemonade/OpenScPCA-analysis/discussions/628
### Describe the goals of the changes to the analysis module.
The goal in this section is to explore and improve the clustering for Wilms tumor samples in `SCPCP000014`.
- I tried an alternative feature selection method [SAM](https://elifesciences.org/articles/48994)
- I utilized the clustering function in this repo [`calculate-clusters.R`](https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/main/packages/rOpenScPCA/R/calculate-clusters.R).
- I explored clustering by looking at anchor transfer results I generated before.
### What will your pull request contain?
R script to run [SAM](https://elifesciences.org/articles/48994) algorithm across 10 samples.
R markdown to explore clustering.
### Will you require additional software beyond what is already in the analysis module?
[SAM](https://elifesciences.org/articles/48994) and its dependencies, which would be installed in a conda environment.
### 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?
This section depends on results generated from anchor transfer. I would create a PR as soon as https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/836 is merged.
Contributor guide
Research direction
Start with the linked Discussion 628 and the clustering implementation in packages/rOpenScPCA/R/calculate-clusters.R. Review the results from anchor transfer and the dependency on pull request 836, then examine the proposed SAM approach across the 10 samples. Done means an R script and R Markdown analysis documenting the clustering exploration and improvement.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100