Question: Which package to use for clustering with UMAP?
gravatar for glabella85
7 weeks ago by
glabella850 wrote:


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!

clustering • 160 views
ADD COMMENTlink written 7 weeks ago by glabella850
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