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.