We wanted to let list members know that there is a new general framework for performing flow cytometry data analysis in R. The package is called openCyto. The framework has the following features
- Importing and analyze manually gated data from FlowJo workspace files using the flowWorkspace package.
- Publication quality plots through flowViz integration.
- Integrated with core flow packages flowCore, flowStats.
Construct re-usable, staining-panel specific templates for automated, data-driven gating defined in a csv (comma separated value) format.
Support for large data sets through disk-backed data structures utilizing HDF5 through the ncdfFlow package.
The OpenCyto framework is going to deprecate the workflow infrastructure for flow cytometry in the future, so it will be worth learning how to use it if you are currently familiar with workflows for flow analysis.
The framework integrates with downstream data analysis packages like COMPASS and MIMOSA.
More information can be found in the vignette and at the website opencyto.org).
The paper describing the package can be found at Plos Computational Biology
Greg Finak, PhD
Fred Hutchinson Cancer Research Center