Figure 1:

The main stages of single-cell analysis, separated broadly into the upper and lower stages of pre-processing and downstream analysis, respectively. Top: The 2 main routes to generating a count matrix from sequencing data: via 1-click quantification solutions or through manual demultiplexing. Bottom: The 4 main stages required to perform cluster-based analysis from the count matrix, through filtering, normalization, confounder removal, and embedding.