To test the scalability of key steps in the Signac workflow, we downsampled the total number of cells in the BICCN dataset and the PBMC scATAC-seq dataset. We downsampled the PBMC dataset from 25,000 cells down to 1,000 cells and the BICCN dataset from 700,000 cells down to 50,000 cells. We randomly sampled different cell numbers from the full dataset and used the FilterCells function in Signac to create downsampled fragment files containing only the cells sampled. We then ran CreateFragmentObject to construct the object required for an analysis in Signac, followed by FeatureMatrix, GeneActivity, NucleosomeSignal, TSSEnrichment, RunTFIDF and RunSVD on each downsampled dataset and recorded the total runtime for each step. For steps able to be run in parallel, we tested these with 1, 2, 4 and 8 cores.
