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New single‐cell technologies readily permit gene expression profiling of thousands of cells at single‐cell resolution. In this review, we will discuss methods for visualisation and interpretation of single‐cell gene expression data, and the computational analysis needed to go from raw data to predictive executable models of gene regulatory network function. We will focus primarily on single‐cell real‐time quantitative PCR and RNA‐sequencing data, but much of what we cover will also be relevant to other platforms, such as the mass cytometry technology for high‐dimensional single‐cell proteomics.