There are many packages on Bioconductor, CRAN and GitHub to build and improve workflows. Here are the essentials.

Rafael Gottardo leads a fabulous team (Greg Finak, Mike Jiang, Jake Wagner) that develops the core packages for flow cytometry. These packages provide examples (vignettes). Looking at the results of those packages is valuable, at least to know what is possible. The team is also building cytoverse, an aggregate of package to ease loading packages.

Packages from Robinson’s lab and Saeys’s lab are presented in the post dedicated to workflows.

Ryan Brinkman proposes flowDensity, RchyOptimyx and others packages.

Dillon Hammill set up the CytoExplorerSuite. This library eases visualizing and gating cells: « To ease the transition from GUI oriented software, CytoExploreR has been designed to be a consistent and auto-complete friendly package for cytometry data analysis ».

An overview of packages and tools ia available at the Biosurf resource.