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The github-pages site documentation is a bit outdated.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.