Skip to content

jiang-junyao/IReNA

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

IReNA: integrated regulatory network analysis of single-cell transcriptomes

Significance of IReNA

There are several cell states involved in cell development or disease occurrence (e.g., progenitor, precursor, immature, and mature), each state maintained by a unique gene program (gene regulatory modules). Decoding the inter- or intra-regulatory mechanisms among these modules can further elucidate the key mechanisms that regulate cell state transitions, including identifying key transcription factors that regulate cell fate decisions or cell differentiation. Most current gene regulatory network (GRN) analysis methods focus on intra-modular regulations; they select all cell states or single cell states to construct GRNs and neglect inter-modular regulations.

IReNA can address this gap by identifying transcription factors (TFs) that regulate other modules and inferring inter-modular interactions through hypergeometric tests. For instance, if IReNA identifies TF A from module a significantly activating module b, we can infer that TF A may regulate the differentiation of the progenitor state into the precursor state. In a second case, if IReNA identifies TF B from module c significantly repressing module d, we can infer that TF B represses the differentiation process from the immature state to the mature state.

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

News

2024.11.12: add the signifiance of IReNA and update the workflow.

2024.10.17: add qucik start tutorial at the ReadME page.

Full tutorials

External links

An example of applying IReNA to identify key transcription factors in retinal regeneration

Citation

Jiang J, Lyu P, Li J, et al. IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles. iScience 2022, 25(11): 105359.

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 [email protected]. I will answer you timely, and please remind me again if you have not received response more than three days.

About

R package IReNA

Topics

Resources

License

GPL-3.0, GPL-3.0 licenses found

Licenses found

GPL-3.0
LICENSE
GPL-3.0
LICENSE.md

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages