scMORE (single cell MultiOmics Regulon Enrichment) is designed to identify disease-relevant regulons by leveraging GWAS summary statistics and multimodal single-cell measurements, where gene expression and chromatin accessibility are either measured for each individual cell or integrated into metacell or clusters to capture both modalities. Please find the scMORE R package in [Github] (https://github.com/mayunlong89/scMORE).
Here, we provide all the necessary scripts for reproducing scMORE analyses, including those used for analyzing and visualizing ground-truth datasets, real single-cell multiomics data, and various GWAS summary statistics for complex diseases.
Ma et al., scMORE uncovers cellular context-specific regulomes linked to complex diseases by integrating polygenic signals and single-cell multiomics, In submission 2025
Human organoids are advanced three-dimensional structures that accurately recapitulate key characteristics of human organ development and functions. Unlike two-dimensional cultures lacking critical cell-cell communications, organoids provides a powerful model for recovering complex cellular dynamics involved in developmental and homeostatic processes. Organoids also allow genetic and pharmacological manipulation in a more physiologically relevant context compared to animal models. Although single-cell sequencing advancements have accelerated their biological and therapeutic use, there has been no systematic platform for unified processing and analysis of organoid-based single-cell multiomics data.
We thus established scHOB (single-cell Human Organoid Bank), a multi-omic single-cell database, consisting of both scRNA-seq and scATAC-seq data on 10 types of widely-adopted human organoids (i.e., brain, lung, heart, eye, liver & bile duct, pancreas, intestine, kidney, and skin) spanning more than 1.5 million cells with 67 main cell types in 385 samples across 83 distinct protocols. see Github code; see scHOB Website.
- Ma et al., Integration of human organoids single-cell transcriptomic profiles and human genetics repurposes critical cell type-specific drug targets for severe COVID-19. Cell Proliferation,2024, and see related Github codes.
- Ma et al., Sytematic dissection of pleiotropic loci and critical regulons in excitatory neurons and microglia relevant to neuropsychiatric and ocular diseases, Translational Psychiatry, 2025. preprint version see: Research Square, 2024.
-
Development of novel polygenic regression method scPagwas for integrating scRNA-seq data with GWAS on complex diseases. see Ma et al. Cell Genomics, 2023, and see related Github codes
