Data Analysis Tools and Information
Commercially available software can be used to analyze your CyTOF data. Cytobank, FlowJo and FCS Express will all allow for basic analysis such as bivariate plots, histogram overlays, heatmaps and dose response. Cytobank also offers user-friendly versions of ViSNE, SPADE, and Citrus for analyzing high dimensional data. You will need to download the most current version of FlowJo and FCS Express to accurately view your CyTOF data. Cytobank is also cloud-based so your data can be accessed from any computer, anywhere.
Free software designed for MatLab and R can be downloaded from Nolan Lab and Dana Pe'er Lab. Both sites also offer overviews and instructions for each type of analysis available. ACCENSE, a 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!)