<!-- README.md is generated from README.Rmd. Please edit that file --> # MIRit <img src="man/figures/logo.svg" align="right" height="139" alt="" /> <!-- badges: start --> [](https://github.com/jacopo-ronchi/MIRit) [](https://github.com/jacopo-ronchi/MIRit/issues) [](https://github.com/jacopo-ronchi/MIRit/pulls) [](https://github.com/jacopo-ronchi/MIRit/commits/devel) [](https://www.repostatus.org/#active) [](https://lifecycle.r-lib.org/articles/stages.html#experimental) [-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3) [](https://doi.org/10.1101/2023.11.24.568528) [](https://github.com/jacopo-ronchi/MIRit/actions/workflows/check-bioc.yml) [](https://app.codecov.io/gh/jacopo-ronchi/MIRit?branch=devel) <!-- badges: end --> ## 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** <a itemprop="sameAs" content="https://orcid.org/0000-0001-5520-4631" href="https://orcid.org/0000-0001-5520-4631" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon"></a>¹ (author and maintainer) **Dr. Maria Foti** <a itemprop="sameAs" content="https://orcid.org/0000-0002-4481-1900" href="https://orcid.org/0000-0002-4481-1900" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon"></a>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](https://github.com/jacopo-ronchi/MIRit) with: ``` r 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](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 *[usethis](https://CRAN.R-project.org/package=usethis)*, *[remotes](https://CRAN.R-project.org/package=remotes)*, and *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized to use [Bioconductor’s docker containers](https://www.bioconductor.org/help/docker/) and *[BiocCheck](https://bioconductor.org/packages/3.19/BiocCheck)*. - Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and *[covr](https://CRAN.R-project.org/package=covr)*. - The [documentation website](http://jacopo-ronchi.github.io/MIRit) is automatically updated thanks to *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*. - The code is styled automatically thanks to *[styler](https://CRAN.R-project.org/package=styler)*. - The documentation is formatted thanks to *[devtools](https://CRAN.R-project.org/package=devtools)* and *[roxygen2](https://CRAN.R-project.org/package=roxygen2)*. This package was developed using *[biocthis](https://bioconductor.org/packages/3.19/biocthis)*.