chromVAR analysis is highly robust to low sequencing depth and readily scales to hundreds or thousands of cells or samples. Budget-constrained researchers often face a trade-off between the number of samples to sequence and the sequencing depth for each sample; sparse sequencing analysis coupled with chromVAR analysis may enable new applications of “bulk” ATAC, DNase-seq or other epigenomic methods as large-scale screening tools. We also anticipate that chromVAR will enable additional downstream analyses of single cell chromatin accessibility data, as the reduction of dimensionality associated with vectors of bias corrected deviations provide a powerful input to existing algorithms for inferring inferring spatial and temporal relationships between cells.
