README.md

In NKInstinct/gater: Interactive Cytometry Gating in R

flowGate: Interactive Manual Gating

Andrew Wight & Harvey Cantor

Dana-Farber Research Institute, Boston, MA

This repository contains the flowGate software package for the R programming language. flowGate is meant to be used within the flow cytometry analysis framework provided by the Bioconductor project and based on the flowCore and (especially) flowWorkspace packages.

flowGate is a simple package that adds an interactive GUI to gating flow cytometry data. This way, you can physically draw rectangle, span, quadrant, and polygon gates on your flow data, once it is read into a GatingSet object using the flowWorkspace package. Please see the vignette accompanying this software package for a step-by-step guide to using flowGate. This vignette was written assuming that the reader has some familiarity with the R programming language, but does not assume that the reader has ever worked with cytometry data in R before. Therefore, the vignette includes a step-by-step guide to performing the necessary data reading steps implemented in flowCore and flowWorkspace before gating, as well as an introduction to plotting flow cytometry data using ggcyto.

flowGate is an ongoing project, so any feedback and suggestions are appreciated. In particular, we hope that the accompanying vignette can act as a clear and concise guide to beginning with flow cytometry analysis in R in general, so suggestions on where to clarify or correct the vignette are always welcome.

Installation Instructions

flowGate can be installed from Bioconductor by running BiocManager::install("flowGate"). Please see the vignette for a more detailed set of steps to install flowGate if you are new to Bioconductor package installation. The devel version can also be installed with devtools::install_github("NKInstinct/flowGate")

Contributions

Contributions to flowGate are always welcome! If there is a bug that needs squishing or a feature you'd like to see added, please open an Issue at github.com/NKInstinct/flowGate. Additionally, if you'd like to contribute code, please fork the repo from github.com/NKInstinct/flowGate and then submit a pull request when finished and we'll see about incorporating your changes.

Please note that flowGate is intended to be approachable to cytometerists regardless of R coding ability, so contributions and suggestions with an eye to making it easier to use or understand are especially welcome!

NKInstinct/gater documentation built on March 18, 2023, 12:42 p.m.