AlexsLemonade / AlexsLemonade/training-modules

include doublet detection in scRNA-seq

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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

Open the contributing 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

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