The Automatic Categorical Gating (AutoCatGate) plugin can be used to quickly and conveniently create gates on parameters with discrete values.
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Background
Parameters with discrete values include: “SampleID”, “Subject”, “AnimalModel”, “Cluster#”, etc. These parameters can be entered manually as numerical annotations within a data matrix, or may be generated during the course of an analysis:
In the case of concatenated data files (separate data files with common parameters combined into a single matrix) SeqGeq will automatically insert the “SampleID” categorical parameter into your data, for convenience in separating these individual files in downstream analyses, and the AutoCatGate plugin makes this separation possible in just a few very simple steps.
Install
Insert the AutoCatGate JAR file into your SeqGeq plugins directory, associated with the software via the Diagnostics preferences in SeqGeq.
Workflow
The plugin will be active in the Plugins section of SeqGeq’s Workspace tab once a population is selected there:
Once selected this plugin will open a user interface where you can select any parameter present in the chosen population:
Running the plugin on any categorical parameter will generate new populations (gates) encompassing events corresponding to all discrete values available in that parameter:
*Note: Seurat is another SeqGeq plugin (illustrated as an example above) which utilizes R packages developed at the Satija Lab.(1)
Any questions regarding SeqGeq’s plugins should be directed to our crack team of application’s specialists: seqgeq@flowjo.com
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