Integrative miRNA-mRNA analysis with MIRit • MIRit

Overview

MIRit (miRNA integration tool) is an open-source R package that aims to facilitate the comprehension of microRNA (miRNA) biology through the integrative analysis of gene and miRNA expression data deriving from different platforms, including microarrays, RNA-Seq, miRNA-Seq, proteomics and single-cell transcriptomics. Given their regulatory importance, a complete characterization of miRNA dysregulations results crucial to explore the molecular networks that may lead to the insurgence of complex diseases. To this purpose, we developed MIRit, an all-in-one framework that provides flexible and powerful methods for performing integrative miRNA-mRNA multi-omic analyses from start to finish.

Authors

Dr. Jacopo Ronchi ¹ (author and maintainer)

Dr. Maria Foti ¹

¹School of Medicine and Surgery, University of Milano-Bicocca, Italy

Installation

MIRit is available on Bioconductor and can be installed using:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("MIRit")

Alternatively, the development version of MIRit can be installed from GitHub with:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("jacopo-ronchi/MIRit")

Usage

For detailed instructions on how to use MIRit for integrative miRNA-mRNA analysis, please refer to the package vignette on Bioconductor. Alternatively, you can refer to the documentation website.

Citation

If you use MIRit in published research, please cite the corresponding paper:

Ronchi, J., & Foti, M. (2026). MIRit: An integrative R framework for the identification of impaired miRNA–mRNA regulatory networks in complex diseases. Bioinformatics Advances, vbag042. https://doi.org/10.1093/bioadv/vbag042

Please note that the MIRit package was made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the MIRit project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.