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README.Rmd
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README.Rmd
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---
title: "IReNA: integrated regulatory network analysis of single-cell transcriptomes"
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%"
)
```
`r badger::badge_custom("r", "version4.04", "green", "https://www.r-project.org")`
`r badger::badge_custom("Seurat", "version4.01", "red", "https://satijalab.org/seurat/articles/get_started.html")`
`r badger::badge_custom("monocle", "version2.18", "blue", "http://cole-trapnell-lab.github.io/monocle-release")`
`r badger::badge_custom("Preprint", "biorxiv", "purple", "https://doi.org/10.1101/2021.11.22.469628")`
IReNA (Integrated Regulatory Network Analysis) is an R package to perform regulatory network analysis. IReNA contains two methods to reconstruct gene regulatory networks. The first is using single-cell RNA sequencing (scRNA-seq) data alone. The second is integrating scRNA-seq data and chromatin accessibility profiles from Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq or bulk ATAC-seq). IReNA performs modular regulatory network to reveal key transcription factors and significant regulatory relationships among modules, providing biological insights on regulatory mechanisms.
## Workflow
{ width=80% height=80% }
## Installation
IReNA needs R version 4.0 or higher, and [Bioconductor](http://bioconductor.org/) version 3.12.
First, install Bioconductor, open R platform and run:
```r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.12")
```
Next, install several Bioconductor dependencies:
```r
BiocManager::install(c('Rsamtools', 'ChIPseeker', 'monocle',
'RcisTarget', 'RCy3', 'clusterProfiler'))
```
Then, install IReNA from GitHub:
```r
install.packages("devtools")
devtools::install_github("jiang-junyao/IReNA")
```
Finally, check whether IReNA was installed correctly, restart R session and run:
```r
library(IReNA)
```
## Examples and tutorials
* [Regulatory network analysis through only scRNA-seq data](https://jiang-junyao.github.io/IReNA/only-scRNA)
* [Regulatory network analysis through intergrating scRNA-seq data and scATAC-seq data](https://jiang-junyao.github.io/IReNA/scATAC+scRNA)
* [Regulatory network analysis through intergrating scRNA-seq data and bulk ATAC-seq data](https://jiang-junyao.github.io/IReNA/bulk-ATAC+scRNA)
## External links
An example for [using IReNA to identify transcription factors critical for retinal regeneration](https://github.com/jiewwwang/Single-cell-retinal-regeneration)
## Citation
Preprint: [IReNA: integrated regulatory network analysis of single-cell transcriptomes](https://doi.org/10.1101/2021.11.22.469628)
[Hoang T, Wang J, Boyd P, et al. Gene regulatory networks controlling vertebrate retinal regeneration. Science 2020; 370(6519):eabb8598](https://www.science.org/doi/10.1126/science.abb8598)
## Help and Suggestion
If you have any question, comment or suggestion, please use github issue tracker to report issues of IReNA or contact <[email protected]>. I will answer you timely, and please remind me again if you have not received response more than three days.