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.
- flowCore provides the core functions to read (and write) FCS files and to handle FCS data in objects that are used by nearly all R packages for cytometry processing (Basic Functions for Flow Cytometry Data).
- openCyto provides an automated data analysis pipeline for flow cytometry. Vignettes are available concerning An Introduction to the openCyto package, How to use different auto gating functions and How to write a csv gating template. cytoqc might be useful to standardize markers name.
- flowWorkspace facilitates comparison of automated gating methods against manual gating done in flowJo. Introduction: A Package to store and maninpulate gated flow data, How to merge GatingSets.
- ggCyto is superseeding flowViz for visualizing cells in coordination with openCyto. Look at Feature summary of ggcyto, Quick plot for cytometry data, Visualize flowSet with ggcyto, Visualize GatingSet with ggcyto.
- CytoML (a GatingML Interface for Cross Platform Cytometry Data Sharing), FAUST, COMPASS, MIMOSA…
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.