RWireX is a R software package that provides various functions to analyze co-accessibility in scATAC-seq data. It is implemented as an extension to the ArchR software package (Granja et al. 2021) building on its existing funcitonalities and is based on our previous work (Mallm et al. 2019). RWireX offers two distinct workflows to uncover different aspects of chromatin organization:
- Single cell co-accessibility workflow:
Identifies autonomous links of co-accessibility (ACs) by analyzing stochastic accessibility changes in individual cells. - Metacell co-accessibility workflow:
Detects domains of contiguous co-accessibility (DCs) using aggregated profiles (metacells) from cells with similar chromatin accessibility.
These workflows enable researchers to identify both long-range interactions (ACs) and local domains of contiguous co-accessibility (DCs), providing a comprehensive view of chromatin organization and its relationship to gene regulation. Key features:
- Compatible with ArchR-processed scATAC-seq data
- Flexible analysis options for different experimental designs
- Visualization tools for co-accessibility matrices
- Statistical methods to assess the significance of identified features
RWireX has been validated on data from various cellular systems, including human endothelial cells, mouse embryonic stem cells, and leukemia models. It is particularly effective with deep coverage scATAC-seq data (≥20,000 unique fragments/cell). A test data set of 200 cells is available at https://www.doi.org/10.5281/zenodo.13142236. For further details on RWireX see our bioRxiv preprint by Seufert et al. By uncovering ACs and DCs, RWireX provides valuable insights into the chromatin-level mechanisms coordinating gene expression programs, applicable to a wide range of biological questions and model systems.
Install required packages:
install.packages("devtools")
install.packages("BiocManager")BiocManager::install("plotgardener")devtools::install_github("GreenleafLab/ArchR", repos = BiocManager::repositories())
ArchR::installExtraPackages()devtools::install_github("dozmorovlab/SpectralTAD")Install RWireX:
devtools::install_github("RippeLab/RWireX")You will need additional genome annotations for visualization.
For human hg38 genome:
BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")
BiocManager::install("org.Hs.eg.db")For mouse mm10 genome:
BiocManager::install("TxDb.Mmusculus.UCSC.mm10.knownGene")
BiocManager::install("org.Mm.eg.db")We provide test data from untreated and 30 min/240 min TNFa-treated HUVECs to run the vignette. The test data is approximately 0.6 GB in size.
library(RWireX)
data_paths <- downloadVignetteData()We provide vignettes as well as extended explanations on how to run single cell as well as metacell co-accessibility workflows in our wiki.
Seufert I, Gerosa I, Varamogianni-Mamatsi V, Vladimirova A, Sen E, Mantz S, Rademacher A, Schumacher S, Liakopoulos P, Kolovos P, Anders S, Mallm JP, Papantonis A, Rippe K (2024) Two distinct chromatin modules regulate proinflammatory gene expression. bioRxiv, 2024.2008.2003.606159, doi: https://doi.org/10.1101/2024.08.03.606159
Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D, Rippe K (2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks. Mol Syst Biol 15, e8339. doi: https://doi.org/10.15252/msb.20188339
Granja, J.M. et al. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat Genet 53, 403-411 (2021).