Implement methods for ambient RNA removal

nf-core / scdownstream

A single cell transcriptomics pipeline for QC, integration and making the data presentable

https://nf-co.re/scdownstream

MIT License

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Implement methods for ambient RNA removal #25

Closed nictru closed 2 weeks ago

nictru commented 3 weeks ago

Description of feature

decontX has already been implemented. The following methods also look interesting:

### Tasks
- [ ] https://github.com/nf-core/scdownstream/issues/26
- [ ] https://github.com/nf-core/scdownstream/issues/27
- [ ] https://github.com/nf-core/scdownstream/issues/31

grst commented 3 weeks ago

There's also scAR which is a newer, autoencoder-based method.

Here's a benchmark paper that recommends cellbender, but also argues that most downstream tasks do not benefit from ambient RNA removal (except for manual cell-type annotation).