README.md

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 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")

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 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.

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.

Development tools

• 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.