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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
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Cell type abbreviation of mouse.rnaseq #105

Closed lambdamoses closed 5 years ago

lambdamoses commented 5 years ago

I used mouse.rnaseq reference with SingleR to coarsely annotate cell types for mouse brain data. So far, I've only been guessing the meanings of the abbreviations. Here's what I guessed:

NPCs: Neural progenitor cells OPCs: Oligodendrocyte progenitor cells aNSCs: Active neural stem cells qNSCs: Quiescent neural stem cells

Please correct me if I'm wrong. I'm especially confused by aNSCs, since it sometimes means adult neural stem cells, and sometimes activated neural stem cells.

dviraran commented 5 years ago

Good guesses :)

aNSC are active neuronal stem cells. You can find all details in this paper - http://m.genome.cshlp.org/content/early/2019/03/11/gr.240093.118 (supp fig 7)

lambdamoses commented 5 years ago

Would you please put the meanings of the abbreviations and the source of the data in the documentation?

dviraran commented 5 years ago

@friedue is working on putting the references in ExperimentHub and a website that allows to explore them. it makes sense that the full names will be there somewhere.

friedue commented 5 years ago

That's a very good point. To be correct, I am not as of yet working on "a website that allows to explore them", it is my wish to have that site, yes, but that's not to say that this is going to magically appear any time soon (I'm sure there are people more suited for that task, too :) )

Anyway, we should absolutely think about how keep track of these details, the easiest might actually be to annotate the colData and to simply add a verbose description of the labels.