TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

Nucleic Acids Res. 2016 Jul 27;44(13):e117. doi: 10.1093/nar/gkw430. Epub 2016 May 13.


When analyzing single-cell RNA-seq data, constructing a pseudo-temporal path to order cells based on the gradual transition of their transcriptomes is a useful way to study gene expression dynamics in a heterogeneous cell population. Currently, a limited number of computational tools are available for this task, and quantitative methods for comparing different tools are lacking. Tools for Single Cell Analysis (TSCAN) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis. TSCAN uses a cluster-based minimum spanning tree (MST) approach to order cells. Cells are first grouped into clusters and an MST is then constructed to connect cluster centers. Pseudo-time is obtained by projecting each cell onto the tree, and the ordered sequence of cells can be used to study dynamic changes of gene expression along the pseudo-time. Clustering cells before MST construction reduces the complexity of the tree space. This often leads to improved cell ordering. It also allows users to conveniently adjust the ordering based on prior knowledge. TSCAN has a graphical user interface (GUI) to support data visualization and user interaction. Furthermore, quantitative measures are developed to objectively evaluate and compare different pseudo-time reconstruction methods. TSCAN is available at https://github.com/zji90/TSCAN and as a Bioconductor package.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology
  • Gene Expression Regulation
  • Genetic Heterogeneity
  • High-Throughput Nucleotide Sequencing
  • RNA / genetics*
  • Single-Cell Analysis / methods*
  • Software*
  • Transcriptome / genetics*
  • User-Computer Interface


  • RNA