TSCAN

TSCAN is a computational tool to reconstruct pseudo-temporal paths in single-cell RNA-seq data analysis. It aims to order cells based on the gradual changes in their transcriptomes, enabling the study of gene expression dynamics within a heterogeneous cell population. TSCAN employs a cluster-based minimum spanning tree (MST) approach, where cells are first grouped into clusters, and then an MST is constructed to connect the cluster centers. The pseudo-time is determined by projecting each cell onto the tree, resulting in an ordered sequence of cells that can be used to investigate dynamic gene expression changes along the pseudo-time.

By clustering cells before constructing the MST, TSCAN reduces the complexity of the tree space, often leading to improved cell ordering and allowing users to adjust the ordering based on prior knowledge. The tool features a graphical user interface (GUI) to facilitate data visualization and user interaction. Additionally, TSCAN introduces quantitative measures for objectively evaluating and comparing different pseudo-time reconstruction methods.