openCyto [<img src="logo_mid.png"/>](http://github.com/RGLab/openCyto) ======== [](https://github.com/RGLab/openCyto/actions) 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 ## Documentation Resources The [github-pages](http://opencyto.org) site documentation is a bit outdated. The [package vignettes](http://www.bioconductor.org/packages/devel/bioc/html/openCyto.html) are the current best resource to get started with the openCyto. - [An introduction to the openCyto package](https://bioconductor.org/packages/devel/bioc/vignettes/openCyto/inst/doc/openCytoVignette.html) - [How to use different auto gating functions](https://bioconductor.org/packages/devel/bioc/vignettes/openCyto/inst/doc/HowToAutoGating.html) - [How to write a csv gating template](https://bioconductor.org/packages/devel/bioc/vignettes/openCyto/inst/doc/HowToWriteCSVTemplate.html) 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.