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berenslab / rna-seq-tsne

The art of using t-SNE for single-cell transcriptomics
GNU General Public License v3.0
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R Implementation for novice #2

Closed iwillham closed 5 years ago

iwillham commented 5 years ago

I have some experience using R (no Python unfortunately) but am having some trouble figuring out how to implement your t-SNE pipeline. In the preprint, you mention that it should be relatively easy to implement in R. What would you recommend as a general approach? Using a Python interface package like reticulate to run the Python functions? Writing an R script de novo to accomplish the same tasks as in the tutorial? Something else?

I found your explanation of the appropriate uses of t-SNE and tradeoffs in parameter selection to be very intuitive. I hope to work this approach into my normal analysis routine for sc-RNA-Seq data. Any help would be greatly appreciated. Thanks!

dkobak commented 5 years ago

@iwilliams91 I am sorry, I haven't noticed your question until right now! Forgot to subscribe to issues. My apologies.

We are using FIt-SNE, and it has R wrapper that is very similar to the Python wrapper. So you can just follow the same steps in R. Let me know if you have more specific questions.

dkobak commented 5 years ago

Closed due to inactivity.