-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.Rmd
83 lines (56 loc) · 5.4 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# 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><sup>1</sup> (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><sup>1</sup>
<sup>1</sup>School 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 'install', 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](). 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')`.