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Matt Regner edited this page Sep 4, 2025 · 13 revisions

Welcome to the scBreast_scRNA_scATAC_2024 wiki!

Herein, we provide documentation of the code used for the analyses presented in "Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic And Transcriptome Profiling". Each page on the right describes which scripts were used in the making of each figure.

Docker container to help replicate the computational environment

R scripts were run in a Docker container executed with Singularity in an HPC environment.

To help users replicate our computational environment (collection of specific software packages and versions), we have uploaded the Docker image to DockerHub for public access: https://hub.docker.com/r/regnerm/scbreast_2023.

To pull the latest version of the Docker image, you may run the following command:

docker pull regnerm/scbreast_2023:1.8.0

Data availability

Processed data available at GEO (https://www.ncbi.nlm.nih.gov/geo/).

Raw data available with controlled access at dbGaP (https://www.ncbi.nlm.nih.gov/gap/).

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