This configuration file contains all parameters for a pipeline run.
This configuration file contains all cell type information needed to generate counts file of all possible marker combinations that represent cell types. It can be manually created or auto-generated based on *CellTypes.xlsx file in meta data directory.
A marker configuration file contains all information needed to run area/density analyses and to plot results. Info includes marker sets (e.g., exhaustion, identity, etc.), marker combinations to plot for each set, and labels to use on plots.
A plot configuration file is used in conjunction with a marker config file to indicate which colors to use for certain marker combinations represented by labels in marker config.
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