Cytometry analysis: viSNE, SPADE, & Heatmaps

These slides are from an advanced cytometry data analysis course based on the methods recently published (Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data. Diggins KE, Ferrell PB, Irish JM, Methods. 2015.).  Please cite this manuscript when referencing this course or methods from it, such as sequential analysis with multiple tools and related modular, unsupervised workflows.

This course was taught at the 2015 Australasian Cytometry Society (ACS) meeting in a master class by Jonathan Irish.  The slides and course content were developed by Jonathan Irish, Kirsten Diggins, & Brent Ferrell.  All materials, images, and slides are copyright (c) 2015 by Jonathan Irish, All Rights Reserved.

This course uses a free trial of Cytobank and publicly available data to go through data analysis with viSNE, SPADE, and heatmaps in Cytobank and R.  All of the starting and intermediate files are available online as well as instructions and slides providing context.

Cytometry analysis with viSNE, SPADE, and heatmaps

A PDF of the images below is available here:

2015-10 Methods Course Diggins Perth – Advanced Clustering Approaches v3 – shown – deanimated v2

All the FCS files are available on Cytobank.  You can sign up for a free 1 month trial to get access to viSNE, SPADE, and more here:

(Note Cytobank is commercial software developed by Dr. Irish and others at Cytobank Inc.)

An experiment containing all the course materials is here on the Premium Cytobank server: