AlexsLemonade / AlexsLemonade/training-modules

Talk about scRNA-seq memory usage and rm()

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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

Open the contributing 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

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