Pseudotime Reconstruction Using TSCAN

Zhicheng Ji, Hong Kai Ji

Research output: Contribution to journalArticle


In many single-cell RNA-seq (scRNA-seq) experiments, cells represent progressively changing states along a continuous biological process. A useful approach to analyzing data from such experiments is to computationally order cells based on their gradual transition of gene expression. The ordered cells can be viewed as samples drawn from a pseudo-temporal trajectory. Analyzing gene expression dynamics along the pseudotime provides a valuable tool for reconstructing the underlying biological process and generating biological insights. TSCAN is an R package to support in silico reconstruction of cells' pseudotime. This chapter introduces how to apply TSCAN to scRNA-seq data to perform pseudotime analysis.

Original languageEnglish (US)
Pages (from-to)115-124
Number of pages10
JournalMethods in molecular biology (Clifton, N.J.)
StatePublished - Jan 1 2019


  • Bioinformatics
  • Gene expression
  • Genomics
  • Minimum spanning tree
  • Pseudotime
  • Single-cell RNA-seq

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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