Introduction to viSNE in Cytobank

Background

viSNE is a tool for reducing high-parameter biological data down to two dimensions. viSNE in Cytobank uses the Barnes-Hut implementation of the t-SNE algorithm (van der Maaten, 2014). Read more about viSNE in this publication from the Pe’er lab at Columbia University:
viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

A viSNE analysis can be run on a data set by logging into Premium or Enterprise Cytobank and using the Experiment Navigation bar to open the viSNE menu and create a new analysis.

The default parameters for viSNE in Cytobank are as follows:

  • perplexity = 30
  • theta = 0.5
  • iterations = 1000

 

Video Overview

(How to set up a viSNE run on an example dataset)

 

 

Document Overview (PDF)

Check out the PDF guide for viSNE analysis.



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