Content - Collection of themes

shawntanzk / cl-manuscript

repo to handle CL manuscript

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Content - Collection of themes #9

Open shawntanzk opened 3 months ago

shawntanzk commented 3 months ago

I think it will be useful for us to collect themes/stories we want to consider writing about in the content section of the paper. Opening this ticket to collect this. I think we can have a discussion below and I'll organise it in the top level of the discussion :)

shawntanzk commented 3 months ago

pinging @gouttegd and @aleixpuigb

shawntanzk commented 3 months ago

Neuro cell types: 1) BDSO stuff - story on how from transcriptomic types, we derive "classical" types to classify 2) Retinal stuff - might need input on this - I know I did add them, but its awhile ago and I got a lot of help there.

shawntanzk commented 3 months ago

I tried to visualise stuff using a few methods, none of them worked well because new classes are very leafy, and if we add all their parentage all the way up, we have the full graph which will not be useful. I am sure there are ways we can do some more complex stuff, but I am not knowledgeable enough to do that. So in the end I just got a subset out and viewed the tree on protege and try to figure out what patterns I can see

Other general stuff I have noticed: 1) Kidney cell types (I assume this is from HCA stuff?) 2) Intestinal cell types 3) Immune cell types (I am guessing this is what @addiehl wrote about)

dosumis commented 3 months ago

To illustrate:

Cell types found by single cell that were then mapped back to a specific location/morphology by imaging. Potential examples - Kidney tubule; Retina; new gut cells?

AvolaAmg commented 1 month ago

Happy to fill in the neuroscience stories once I am back from annual leave