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ktrns / scrnaseq

Workflow for single-cell RNA-seq analysis using Seurat
MIT License
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Feature request: defining ground truths #106

Open semenko opened 2 years ago

semenko commented 2 years ago

Thanks so much for this incredible work!

I'd love to see (if you're adding features), options to define ground ground truths based on known marker genes, outside just file_known_markers — or perhaps an option to derive file_known_markers from celldex?

I'm currently using Seurat v4 Azimuth (which unfortunately only has a few good reference databases available) and/or singleR, which has a nice workbook.

ktrns commented 2 years ago

Dear @semenko,

Thanks so much for your positive feedback, and your suggestion. Are you actively using our workflow?

There are a few features that we would like to add in the future, and mapping cells to a reference is a great point. You can always join our efforts of course!

Best wishes Katrin

kosankem commented 2 years ago

Similar to the issue https://github.com/ktrns/scrnaseq/issues/46, I have put together a small R markdown script which is using the output of the scrnaseq script and performs cluster annotation with reference datasets using SingleR and Clustifyr subsequently. I can also share that with you if it is of any help.

semenko commented 2 years ago

Thanks! I've started using the workflow -- it's great!

I plan to expand use of it in January with a much larger sample set. My end game involves using EcoTyper to define cellular communities -- which requires ground truth annotations of key cell populations (e.g. "B.cells", "Epithelial.cells", etc., details here).

I'm also trying to apply a recent ML model Pollock to label things more cleanly. If things work out nicely I might make a PR.

@kosankem That script would definitely be helpful, if you're able to share.

kosankem commented 2 years ago

@semenko, I apologize for the late reply. You can find a updated version of the annotation_with_reference script under https://github.com/MHH-RCUG/scrnaseq_modular_extensions. I would be glad to hear your feedback.