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For more general information on the CAPX workflow, please see https://sydneycytometry.org.au/capx.
For a usage protocol for the CAPX scripts, please see https://github.com/sydneycytometry/CAPX/wiki/1.-CAPX-R-script-usage-protocol.
For a protocol to follow up CAPX analysis to perform annotation, generate summary data, and create plots or heatmaps, see https://github.com/sydneycytometry/CAPX/wiki/2.-CAPX-follow-up---annotation,-generate-summary-data,-plotting,-and-heatmaps.