page_title: Single-cell transcriptomics
section_title: Pseudotemporal ordering
hierarchical_section_title: Single-cell transcriptomics / Data analysis / Pseudotemporal ordering
context_page_description: Single-cell transcriptomics examines the gene expression level of individual cells in a given population by simultaneously measuring the messenger RNA concentration of hundreds to thousands of genes.
  The unraveling of heterogenous cell populations, reconstruction of cellular developmental trajectories, and modeling of transcriptional dynamics — all previously masked in bulk transcriptome measurements — are made possible through analysis of this transcriptomic data.
context_section_description: Pseudo-temporal ordering (or trajectory inference) is a technique that aims to infer gene expression dynamics from snapshot single-cell data. The method tries to order the cells in such a way that similar cells are closely positioned to each other. This trajectory of cells can be linear, but can also bifurcate or follow more complex graph structures. The trajectory therefore enables the inference of gene expression dynamics and the ordering of cells by their progression through differentiation or response to external stimuli.
  The method relies on the assumptions that the cells follow the same path through the process of interest and that their transcriptional state correlates to their progression. The algorithm can be applied to both mixed populations and temporal samples.
  More than 50 methods for pseudo-temporal ordering have been developed, and each has its own requirements for prior information (such as starting cells or time course data), detectable topologies, and methodology . An example algorithm is the Monocle algorithm that carries out dimensionality reduction of the data, builds a minimal spanning tree using the transformed data, orders cells in pseudo-time by following the longest connected path of the tree and consequently labels cells by type. Another example is DPT, which uses a diffusion map and diffusion process.
caption: Graph with minimal spanning tree