An R package that providing an automated data analysis pipeline for flow cytometry.

CytoML can be installed in several ways:

For all versions, you must have dependencies installed

library(BiocManager)
# This should pull all dependencies for release version of `openCyto`.
BiocManager::install("openCyto") 

# Then install latest dependencies from github, using devtools.
install.packages("devtools") 
library(devtools) #load it
install_github("k-motwani/openCyto", version = "RGLab")

# Or, if you use renv (preferred, personally):
renv::install("k-motwani/openCyto@RGLab")

• Use the issue template in github when creating a new issue.
• Follow the instructions in the template (do your background reading).
• Search and verify that the issue hasn't already been addressed.
• Check the Bioconductor support site.
• Make sure your flow packages are up to date.
• THEN if your issue persists, file a bug report.

Otherwise, we may close your issue without responding.

The github-pages site documentation is a bit outdated.

The package vignettes are the current best resource to get started with the openCyto.

• An introduction to the openCyto package
• How to use different auto gating functions
• How to write a csv gating template

The add_pop() API is a good interactive approach to building up a template, population by population. It takes arguments found in the csv template, performs the gating of a GatingSet or GatingHierarchy and returns a line of text that can be added to a csv template.