What should I do when I have more than two treatments

[QuietgraceH]

Thank you for developing this tool. It is very useful. When I analyze data, there are multiple treatments. When running the tool, I set more than 2 treatments in "comparisonTreatments" in config.json. I hope to compare each treatment with each other. I hope that all "networkTreatment" parameters are involved. However, an error message is reported when running the command. Is there any solution? Thank you again. The following is the error message
Traceback (most recent call last): File "/data/houjy/software/tkna/reconstruction/run.py", line 66, in <module> network_reconstructor.reconstructNetwork(config, dataset, start=args.start, stopStage=args.stop, dataOutFilePath=args.outFile, cores=args.cores) File "/data/houjy/software/tkna/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 749, in reconstructNetwork return self.runPipeline(stages, allData, **kwargs) File "/data/houjy/software/tkna/reconstruction/reconstruction/NetworkReconstructor.py", line 59, in runPipeline stage(allData) File "/data/houjy/software/tkna/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 673, in computeDifferences allData["differencePValues"] = computeDifferencePValues(config, allData["originalData"], data.get_object("pairings", absent_ok=True)) File "/data/houjy/software/tkna/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 130, in computeDifferencePValues raise Exception("More than 2 treatments given to compare") Exception: More than 2 treatments given to compare

[QuietgraceH]

@newmanno

[QuietgraceH]

When I was looking at the help just now, I found that I could use the "--singlecell" parameter, but I didn't find a corresponding demo example. Could you give me an example? I hope to analyze at the cluster level. Thank you.

[QuietgraceH]

@macovskym @newmanno Thank you for your reply when you are free.