Differential Co-Localization analysis (DiCoLo) is a computational framework designed for capturing condition-specific co-localized gene patterns within single-cell RNA sequencing data. The major workflow of DiCoLo comprises the following three main steps:
- Step1. Compute gene-gene OT distance for each condition
- Step2. Construct differential graph operator
- Step3. Identify differential co-localized genes by spectral analysis
- Downstream tasks
- Assemble significant DiCoLo genes into co-localized gene modules.
Installation
DiCoLo can be installed in R as follows:
install.packages("devtools")
devtools::install_github("KlugerLab/DiCoLo")
library("DiCoLo")Example tutorial
Please check DiCoLo tutorial.
References
References of DiCoLo functions can be found here.
For additional information, please reference our pre-print:
DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data Ruiqi Li, Junchen Yang, Pei-Chun Su, Ariel Jaffe, Ofir Lindenbaum, Yuval Kluger bioRxiv 2025 November 26. doi: https://doi.org/10.1101/2025.11.23.689932