Which package to use for clustering with UMAP?

Question

[glabella85]

Hello,

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!

Answer 1

[steveh]

I've been using Seurat successfully over the last few weeks for single-cell RNA-seq, along with SCTransform to perform the normalisation step.

A tutorial for SCTransform is here:

https://rawgit.com/ChristophH/sctransform/master/inst/doc/seurat.html

and that might be all you need, or otherwise a longer tutorial on seurat (but not including SCTranform) is here:

https://satijalab.org/seurat/seurat_clustering_tutorial_part1.html https://satijalab.org/seurat/seurat_clustering_tutorial_part2.html

unfortunately there's no GUI though I'm afraid, it's all just coding in R. Hope that helps!