This repository contains the code used for the visualization and analysis of single-cell transcriptomics and 10X multiomics datasets related to the publication. Processed datasets are uploaded to GEO under the accession numbers GSE282228 for 10X multiome and GSE281982 for scRNA-seq.

The operating system used for performing all the analysis is Linux Ubuntu 18.04. R version is 4.4.2. Information about the versions of the packages used for each analysis is included in the Methods section of the manuscript. Information regarding each code is included as a header.

For running SCENIC and SCENIC+, conda environment has been built. Environment for SCENIC and SCENIC+ is available.

Installation of packages are followed as what the developers recommended. If the R package is removed from the repository, the formerly available versions are obtained from the archive and installation was done manually.

Annotated seurat data object and related files which are used for publications are available upon request.

• Cédric Blanpain (Corresponding author): [email protected]
• Alexandra Van Keymeulen (Corresponding author): [email protected]
• Yura Song (Bioinformatician): [email protected]