AlexsLemonade / AlexsLemonade/training-modules
include doublet detection in scRNA-seq
- Dominant language
- HTML
- Stars
- 77
- Forks
- 35
- Avg merge
- 18h 38m
- Merged PRs (30d)
- 3
Description
From a question about removing high-transcript count cells from scRNA-seq as part of QC, we realized that we do not cover the question of detecting cell doublets in our modules. This should be added, using either tools in `scran` or other techniques.
It may also be useful to discuss the question of barcode multiplets, which has received less attention, but can also potentially bias results.
Some references:
https://osca.bioconductor.org/doublet-detection.html
https://www.cell.com/cell-systems/fulltext/S2405-4712(20)30195-2
https://www.nature.com/articles/s41467-020-14667-5
Contributor guide
Research direction
Review the existing scRNA-seq QC modules and the linked OSCA doublet-detection reference first. Define the coverage for cell doublets and barcode multiplets, select the techniques to discuss, and add the discussion and references to the relevant modules.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, documentation
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100