In jiang-junyao/IReNA: IReNA

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
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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

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Installation

IReNA needs R version 4.0 or higher, and Bioconductor version 3.12.

First, install Bioconductor, open R platform and run:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.12")

Next, install several Bioconductor dependencies:

BiocManager::install(c('Rsamtools', 'ChIPseeker', 'monocle',
                       'RcisTarget', 'RCy3', 'clusterProfiler'))

Then, install IReNA from GitHub:

install.packages("devtools")
devtools::install_github("jiang-junyao/IReNA")

Finally, check whether IReNA was installed correctly, restart R session and run:

library(IReNA)

Examples and tutorials

• Regulatory network analysis through only scRNA-seq data

• Regulatory network analysis through intergrating scRNA-seq data and scATAC-seq data

• Regulatory network analysis through intergrating scRNA-seq data and bulk ATAC-seq data

External links

An example for using IReNA to identify transcription factors critical for retinal regeneration

Citation

Preprint: IReNA: integrated regulatory network analysis of single-cell transcriptomes

Hoang T, Wang J, Boyd P, et al. Gene regulatory networks controlling vertebrate retinal regeneration. Science 2020; 370(6519):eabb8598

Help and Suggestion

If you have any question, comment or suggestion, please use github issue tracker to report issues of IReNA or contact [e-mail]. I will answer you timely, and please remind me again if you have not received response more than three days.

jiang-junyao/IReNA documentation built on May 17, 2024, 12:29 a.m.