aggregateData | Combine feature tables | Details |
selectROIs | Define tissue ROIs | Details |
intensityFilter | Filter out-of-focus and counterstain oversaturated cells | Details |
areaFilter | Filter over- and under-segmented cells | Details |
cycleCorrelation | Filter unstable cells | Details |
logTransform | Log10-transform immunomarker signals | Details |
pruneOutliers | Filter channel outliers | Details |
metaQC | Reclassify cells according to QC status | Details |
PCA | Run principle component analysis | Details |
setContrast | Adjust image contrast settings | Details |
gating | Identify cell states via manual thresholding | Details |
clustering | Identify cell states via unsupervised clustering | Details |
clustermap | Visualize cell state protein expression | Details |
frequencyStats | Compute cluster frequency statistics | Details |
curateThumbnails | Visualize example cells from each cluster | Details |
