openCyto <img src="logo_mid.png"/>

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

Reporting Bugs or Issues

• 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.

Documentation Resources

The github-pages site documentation is a bit outdated.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