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Longo-Lab / Longo-Lab.github.io

https://longo-lab.github.io/
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snRNAseq annotation tutorial #5

Open rbutleriii opened 1 year ago

rbutleriii commented 1 year ago

Need tutorials for general level classification and then a more detailed example for one subclass.

rbutleriii commented 1 year ago

First I will come up with a general outline, and then @cyouh95 can fill in with images and code from our Rmarkdown and Github issues

rbutleriii commented 1 year ago

Current outline:

I. Iterative clustering
   A. Sample pre-processing
      - Cell Ranger, SoupX, DoubletFinder
   B. Integration and clustering
      - Define integration
      - No integration at subclass level
   C. Reference mapping
      - Reference sources
II. Manual annotation
   A. Predicted cell types
   B. Gene markers
      - Table of markers w/ sources
   C. Gene set enrichment
      - gProfiler, Enrichr
   D. Quality/Dying cells
      - Cell count/MT count, etc.
      - Cell death markers
   E. Cluster consistency
      - Location in overall UMAP
      - Heavy spreading may be chimeric
   F. Further subclustering
      - Subclass level only
rbutleriii commented 3 months ago

Need to review and then plan for annotation framework v2.0