TimiRGeN

The software tool 'TimiRGeN' is for the analysis of longitudinal miRNA-mRNA datasets, with a focus on constructing gene regulatory networks (GRNs). Leveraging time point-based differential expression results, TimiRGeN identifies miRNA-mRNA interactions that influence signaling pathways. The tool provides visualization options in R and supports export to PathVisio or Cytoscape, enabling researchers to explore interactions, generate hypotheses, and guide further in vitro or silico analyses, such as GRN construction.

Topic

Molecular interactions, pathways and networks;Functional, regulatory and non-coding RNA;Gene expression;RNA-Seq

Detail

  • Operation: Gene regulatory network analysis;Network visualisation;Differential gene expression profiling;miRNA target prediction

  • Software interface: Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.11.0

  • Credit: The Dunhill Medical Trust, Novo Nordisk Fonden Challenge Programme: Harnessing the Power of Big Data to Address the Societal Challenge of Aging, the MRC and Versus Arthritis as part of the Medical Research Council Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing.

  • Input: -

  • Output: -

  • Contact: Krutik Patel krutik.patel@newcastle.ac.uk

  • Collection: -

  • Maturity: Stable

Publications

  • TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis.
  • Patel K, et al. TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis. TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis. 2021; 37:3604-3609. doi: 10.1093/bioinformatics/btab377
  • https://doi.org/10.1093/BIOINFORMATICS/BTAB377
  • PMID: 33993215
  • PMC: PMC8545325

Download and documentation

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