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Updated: Nov 5, 2025

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
Published on: August 21, 2019
TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis
K Patel1, S Chandrasegaran1, I M Clark2
1Campus for Ageing and Vitality, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE4 5PL, UK.
Motivation:
The analysis of longitudinal datasets and construction of gene regulatory networks (GRNs) provide a valuable means to disentangle the complexity of microRNA (miRNA)-mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal miRNA-mRNA datasets.
Results:
We present TimiRGeN, an R package that uses time point-based differential expression results to identify miRNA-mRNA interactions influencing signaling pathways of interest. miRNA-mRNA interactions can be visualized in R or exported to PathVisio or Cytoscape. The output can be used for hypothesis generation and directing in vitro or further in silico work such as GRN construction.
Availability And Implementation:
TimiRGeN is available for download on Bioconductor (https://bioconductor.org/packages/TimiRGeN) and requires R v4.0.2 or newer and BiocManager v3.12 or newer.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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