Many ways to skin an isotope. What's yours? Data sharing in the form of FCS files and images is encouraged.
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Please be as geeky as possible. Reference, reference, reference. Also, please note that this is a mixed bag of math-gurus and mathematically challenged, so choose your words wisely
I'd recommend starting with the Cytofkit package. It will import your data, run tSNE on it, and it provides a nice graphical interface to view and export the plots. It can also run PhenoGraph clustering on your data and allows you to view those clusters in tSNE space. Just be sure to choose "cytofAsinh" as the scaling factor when you set up the run in the GUI window. I'd recommend starting with 1000 events from a single FCS file until you get the hang of it.
Erin and Mike point out some very nice links to analyze data in R, of course, you can use FlowJo to analyze CyTof data by dragging and dropping, using clustering and t-SNE denoised by PCA, etc. For more information check this out, https://www.flowjo.com/solutions/flowjo/downloads, we have a trial you can sign-up for and technical support to help you.
You might want to look into the flowCore R package, which allows you to import FCS files into R. Once the data is in R, you can use the Rtsne package to run t-SNE on it. This route is relevant if you're looking to build your own pipeline for FCS analysis, if you just want to run t-SNE then the GUI option Erin pointed out might be the way to go.
Thanks for all the recommendations, and glad to see people using cytofkit!
Unfortunately, a bug was identified regarding how clustering was handled in cytofkit, detailed here.
Thankfully, we've fixed the issue and the fix (along with new features) can be accessed by updating cytofkit. To do so, you can update your version of R to 3.4.2 and update to Bioconductor v3.6 then run the following: