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.
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)-
Regulatory network analysis through intergrating scRNA-seq data and scATAC-seq data
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Regulatory network analysis through intergrating scRNA-seq data and bulk ATAC-seq data
An example for using IReNA to identify transcription factors critical for retinal regeneration
IReNA: integrated regulatory network analysis of single-cell transcriptomes
If you have any question, comment or suggestion, please use github issue tracker to report issues of IReNA or contact jiangjunyao@westlake.edu.cn. I will answer you timely, and please remind me gain if you have not received response more than three days.