scMultiMap

scMultiMap is an R package for inferring cell-type-specific peak-gene associations using single-cell multimodal data. It implements the statistical method proposed in article scMultiMap: Cell-type-specific mapping of enhancers and target genes from single-cell multimodal data.

Citation: Chang Su, Dongsoo Lee, Peng Jin and Jingfei Zhang. (2025). scMultiMap: Cell-type-specific mapping of enhancers and target genes from single-cell multimodal data. Nature Communications.

Installation

You can install scMultiMap from GitHub using devtools:

# Load devtools for installing R packages from GitHub
library(devtools)

# Install scMultiMap from GitHub
install_github("ChangSuBiostats/scMultiMap")

Vignettes

The following vignettes provide detailed use cases for scMultiMap:

1. Introduction to scMultiMap: Learn how to infer peak-gene associations in cell types using 10x Multiome data on PBMC.

2. scMultiMap for disease-control studies: Identify differentially associated peak-gene pairs in disease-control studies.

3. scMultiMap for integrative analysis with GWAS results: Integrate scMultiMap results with genome-wide association studies (GWAS) to explore the regulatory roles of GWAS variants in disease-associated cell types.

scMultiMap_analysis for reproducibility

To reproduce the analysis in scMultiMap article, please visit our dedicated GitHub repository containing the source code used in the paper: scMultiMap_analysis.

Contact us

For issues or feature requests, please visit GitHub Issues. If an issue remains unanswered for a while, you are welcome to email the maintainer at chang.su@emory.edu.

Updates

[04/26/2026] Published at Nature Communications.