Official source codes of the GROTIA

This repository holds the official source codes for the paper An Interpretable Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis (GROTIA). It is a framework for joint analysis of unpaired scRNA-seq and scATAC-seq data. It provides two core capabilities:

1. GROTIA learns interpretable, modality-specific embeddings that project RNA and ATAC into a shared low-dimensional space while attaching an importance score to every gene or peak.
2. GROTIA converts the optimal-transport plan into a cross-modal affinity matrix for robust cell co-clustering, powering downstream tasks such as trajectory inference and cell-type annotation.