We have created lots of code (all in R) for the analysis of flow cytometry data. We’re happy to share that code with you freely, or, if it’s not ready to share, to adapt it to your analysis problem in a consulting setting.
Below is a list of R packages that are at a stage where it makes sense to post here. Most of these are in “alpha” development stage. Please feel free to download and kick the tires. Email me if you have comments/questions/suggestions.
| Package | Brief description |
| panoplyCF | t-SNE upon Cytometric Fingerprinting |
| fluster | Fingerprint-based Clustering |
| tailor | Clustering via Gaussian Mixture Modeling on distributions with heavy tails (authored by Matei Ionita at the University of Pennsylvania) |
| HiTMapper | Fast implementation of the mapper network induction algorithm, with Leiden community detection (authored by Matei Ionita at the University of Pennsylvania) |
| wadeTools | A quasi-random collection of useful flow cytometry functions |
| flowMie | Mie Theory modeling of the response of a flow cytometer to small particle light scattering. Handles laser polarization and multi-layer particles (like membrane-enclosed extracellular vesicles). |