Over the last 5 years, single cell methods have enabled the monitoring of gene and protein
expression, genetic, and epigenetic changes in thousands of individual cells in a single
experiment. With the improved measurement and the decreasing cost of the reactions and
sequencing, the size of these datasets is increasing rapidly. The critical bottleneck remains
the analysis of the wealth of information generated by single cell experiments. In this review,
we give a simplified overview of the analysis pipelines, as they are typically used in the field …