Currently I am doing single cell analysis with R.
For tSNE, Cytofkit is what I use and it is quite easy to use since it gives you an GUI from the very beginning.
However, this tool has some limitations because it requires data to be in a .fcs format
and does not accept csv(Our study is protein-based but not flow cytometry).
I've heard that UMAP could directly use csv data and has many
advanced features compared to tSNE in single cell analysis. However, I found several R packages that
has similar traits but was written by different developers. Is there any suggestion on which package I should
use? It would be nice to have a GUI like cytofkit. I hope this question is not so out of place and I thank you in
advance for any recommendations!