SCODE

The software tool SCODE was developed to infer regulatory networks based on ordinary differential equations from RNA-Seq data of individual differentiating cells. SCODE was applied to three single-cell RNA-Seq datasets and demonstrated efficient reconstruction of expression dynamics with high performance in comparison to alternative algorithms.

Topic

RNA-Seq;Gene expression

Detail

  • Operation: RNA-seq analysis

  • Software interface: Command-line user interface

  • Language: R

  • License: The MIT licence

  • Cost: Free

  • Version name: -

  • Credit: Grant-in-Aid for Japan Society for the Promotion of Science (JSPS) Fellows, JSPS KAKENHI, Core Research for Evolutional Science and Technology (CREST) “Creation of Fundamental Technologies for Understanding and Control of Biosystem Dynamics” from the Japan Science and Technology Agency (JST).

  • Input: -

  • Output: -

  • Contact: hirotaka.matsumoto@riken.jp

  • Collection: -

  • Maturity: -

Publications

  • SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.
  • Matsumoto H, et al. SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. 2017; 33:2314-2321. doi: 10.1093/bioinformatics/btx194
  • https://doi.org/10.1093/bioinformatics/btx194
  • PMID: 28379368
  • PMC: 28379368

Download and documentation

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