To profile the time required for an end-to-end analysis of each dataset starting from the raw data (the fragment file) and a set of peaks, we ran the createArrowFiles and ArchRProject functions to create the object in R required for analysis, followed by addPeakSet and addPeakMatrix for quantification, addIterativeLSI and addUMAP for dimension reduction and addClusters for cell clustering. This was performed using eight cores by setting addArchRThreads(threads = 8).
