AlexsLemonade / AlexsLemonade/training-modules
Talk about scRNA-seq memory usage and rm()
- Dominant language
- HTML
- Stars
- 77
- Forks
- 35
- Avg merge
- 1d 13h
- Merged PRs (30d)
- 4
Description
The current scRNA-seq notebook 01 starts to get into pretty high memory usage of ~4Gb with multiple copies of the large count matrix under different filtering conditions, etc. It might be good to add a section about keeping that usage down through judicious use of `rm()` to clear out earlier steps in the pathway. Also a note that on a personal computer, this could be a real limitation.
Contributor guide
Research direction
Start by locating the current scRNA-seq notebook 01 and review where multiple filtered copies of the count matrix are created. Add a section covering judicious use of rm() to reduce memory usage and the limitations of running the notebook on a personal computer; the notebook should clearly communicate these recommendations.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100