AutoSpectralHelper is a Shiny application for building and validating the spectral flow cytometry control files for use in AutoSpectral. It provides an interactive interface for selecting controls, marking unstained samples, editing metadata, and exporting a finalized control file.
- Select cytometer configuration
- Load control files from a directory
- Interactive table editor
- Mark/unmark unstained controls for use as universal negatives
- Reorder controls (helpful for plotting fluorophore spectra later)
- Auto-fill functions
- Export validated control files to the directory of your choosing
Download the app.r file.
Alternatively, run it directly from GitHub:
shiny::runGitHub("AutoSpectralHelper", "DrCytometer")While you can manually install the dependencies, this occurs automatically when you first run the app.
You will need AutoSpectral version 1.5.4 or higher. Just re-install it if you aren't sure.
Install pak if you don't have it.
pak::pak("DrCytometer/AutoSpectral")Place a copy of the app in the folder where you want to work. The app will look for your single-stained control files in this folder, with your assistance.
To launch the app, click the green "Run App" button on the upper right of the app file.
For more details and instructions on creating the control file, visit the help page on AutoSpectral: https://drcytometer.github.io/AutoSpectral/articles/Control_File_example.html
R >= 4.1 AutoSpectral >= 1.5.4 For integration with the newest AutoSpectral pipeline, upgrade AutoSpectral to at least version 1.5.8. Otherwise you will see a "legacy mode" warning. All other requirements are automatically installed on first launch.
If you encounter problems, please open an issue: https://github.com/DrCytometer/AutoSpectralHelper/issues
AGPL (>= 3)