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.

Dr. Jacopo Ronchi ¹ (author and maintainer)

Dr. Maria Foti ¹

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

MIRit is currently undergoing Bioconductor submission. In the meantime, you can install it from GitHub with:

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

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

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.

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

Ronchi J and Foti M. ‘MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases’. bioRxiv (2023). doi:10.1101/2023.11.24.568528

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.

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.

• Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
• Code coverage assessment is possible thanks to codecov and covr.
• The documentation website is automatically updated thanks to pkgdown.
• The code is styled automatically thanks to styler.
• The documentation is formatted thanks to devtools and roxygen2.

This package was developed using biocthis.