mirit

An open-source R package to comprehensively explore the role of impaired miRNA regulatory networks in complex biological conditions.

https://github.com/jacopo-ronchi/mirit

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An open-source R package to comprehensively explore the role of impaired miRNA regulatory networks in complex biological conditions.

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```

# MIRit 


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## 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:

```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("MIRit")
```

Alternatively, the development version of MIRit can be installed from [GitHub](https://github.com/jacopo-ronchi/MIRit) with:

```{r 'installDev', eval = FALSE}
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](https://www.bioconductor.org/packages/release/bioc/vignettes/MIRit/inst/doc/MIRit.html). Alternatively, you can refer to the [documentation website](http://jacopo-ronchi.github.io/MIRit).

## 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](http://bioconductor.org/about/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](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://jacopo-ronchi.github.io/MIRit) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.

This package was developed using `r BiocStyle::Biocpkg('biocthis')`.

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