TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis

Krutik Patel, Sharmilla Chandrasegaran, Ian Clark, Carole Proctor, David Young, Daryl Shanley

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Abstract

Motivation: The analysis of longitudinal datasets and construction of gene regulatory networks provide a valuable means to disentangle the complexity of microRNA-mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal microRNA-mRNA datasets.

Results: We present TimiRGeN, an R package that uses time point based differential expression results to identify miRNA-mRNA interactions influencing signalling pathways of interest. miRNA-mRNA interactions can be visualised 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 gene regulatory network 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.
Original languageEnglish
JournalBioinformatics
Early online date16 May 2021
DOIs
Publication statusE-pub ahead of print - 16 May 2021

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