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Module list

NamePurposeDescription/YAML Configurations
aggregateDataCombine feature tablesDetails
selectROIsDefine tissue ROIsDetails
intensityFilterFilter out-of-focus and counterstain oversaturated cellsDetails
areaFilterFilter over- and under-segmented cellsDetails
cycleCorrelationFilter unstable cellsDetails
logTransformLog10-transform immunomarker signalsDetails
pruneOutliersFilter channel outliersDetails
metaQCReclassify cells according to QC statusDetails
PCARun principle component analysisDetails
setContrastAdjust image contrast settingsDetails
gatingIdentify cell states via manual thresholdingDetails
clusteringIdentify cell states via unsupervised clusteringDetails
clustermapVisualize cell state protein expressionDetails
frequencyStatsCompute cluster frequency statisticsDetails
curateThumbnailsVisualize example cells from each clusterDetails

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