Data Analysis Tools and Information
Commercially available software can be used to analyze your CyTOF data. Cytobank, FlowJo and FCS Express can be used for basic analysis such as bivariate plots, histogram overlays, heatmaps and dose response. Cytobank and FlowJo have plugins, which offer user-friendly versions of clustering algorithms such as ViSNE/tSNE, SPADE, and Citrus for analyzing high dimensional data. Maxpar Pathsetter can be used on MDIPA-stained samples to automatically analyze and identify 37 immune cell types.
Free software designed for MatLab and R can be downloaded from Nolan Lab. They offer overviews and instructions for each type of analysis available. ACCENSE, an alternative tSNE algorithm, is also available for download independently. Premessa is an R script that can be used to edit/rename panels as well as normalize and debarcode FCS files.
Normalization, concatenation, debarcoding, and FCS to TXT is available in the Fluidigm Helios software. This can be done in the core on the instrument computers or the CyTOF data workstation. A freestanding version is available for download online (PC only!)