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

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. SUPPLEMENTARY INFORMATION Supplementary data is available at Bioinformatics online.