SINCERITIES

SINCERITIES (SINgle CEll Regularized Inference using TIme-stamped Expression profileS) is a software tool developed for inferring gene regulatory networks (GRNs) from single cell transcriptional profiles using regularized linear regression and partial correlation analyses. It focuses on time-stamped cross-sectional expression data and recovers directed regulatory relationships among genes. The tool was shown to be effective in inferring GRNs using in silico time-stamped single cell expression data and single cell transcriptional profiles of THP-1 monocytic human leukemia cells. SINCERITIES has a low computational complexity and is available in MATLAB and R versions, with single cell THP-1 and T2EC transcriptional profiles available from the original publications.

Topic

RNA-Seq;Gene expression

Detail

  • Operation: RNA-seq analysis

  • Software interface: Command-line user interface

  • Language: MATLAB/R

  • License: BSD-3-clause

  • Cost: Free

  • Version name: -

  • Credit: Swiss National Science Foundation

  • Input: -

  • Output: -

  • Contact: rudi.gunawan@chem.ethz.ch

  • Collection: -

  • Maturity: -

Publications

  • SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles.
  • Papili Gao N, et al. SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. 2018; 34:258-266. doi: 10.1093/bioinformatics/btx575
  • https://doi.org/10.1093/bioinformatics/btx575
  • PMID: 28968704
  • PMC: 28968704

Download and documentation

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