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carmonalab / ProjecTILs

Interpretation of cell states using reference single-cell maps
GNU General Public License v3.0
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Human TILs ATLAS #2

Closed AteeqMKhaliq closed 4 years ago

AteeqMKhaliq commented 4 years ago

Hi, Thank for making this wounderful package. I am currently having Human cancer single-cell data and i wanted to analyse my data by using ProjecTILS. My question is can I use Default Reference Atlas(Mouse) to analyse Human cancer Single-cell RNAseq data sets? It would be great if you can let me know where can I find the human reference TILs to use with this package. Thanks a lot for your help. Have a great day, Ateeq

sjcarmona commented 4 years ago

Hi Ateeq, thank you for your comment. Currently we provide a reference for mouse T cells only, for which we are confident about all subtypes. A human equivalent atlas is ongoing work. However, you could try an exploratory analysis projecting human T cells using mouse orthologs over the mouse reference. Let us know if you would like to discuss about it

mass-a commented 4 years ago

The development version of ProjecTILs now supports projection of human data onto a mouse reference atlas. Get it with:

remotes::install_git("https://gitlab.unil.ch/carmona/ProjecTILs.git", branch = "v0.4.1")

And then turn on the human.ortho flag when running the projection algorithm, e.g.

query.projected <- make.projection(query.object, ref=ref, human.ortho = T)

Take a look at this case study for a worked-out example.

Cheers! -m