README.md

In jiang-junyao/IReNA: IReNA

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

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

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)

Quick start

• Run IReNA based on seurat object (without pre-build GRN and gene modules)

• Run IReNA based on pre-build GRN and gene modules

NEWs

2024.10.17 add qucik start tutorial at the ReadME page.

Full 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

Official publication: IReNA: integrated regulatory network analysis of single-cell transcriptomes

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 Nov. 4, 2024, 8:29 p.m.