This repository contains code related to data processing and downstream analysis associated with the study "A single-cell and spatially resolved atlas of human breast cancers" at Nature Genetics.
All processed scRNA-seq data and is available for in-browser exploration and download through the Broad Single-Cell portal at https://singlecell.broadinstitute.org/single_cell/study/SCP1039. CITE data can also be downloaded from this portal, although it cannot be explored interactively at this point. Processed data is also available on GEO (GSE176078).
Raw scRNA-Seq data from this study has been deposited in the European Genome-Phenome Archive (EGA), which is hosted by the EBI and the CRG, under the accession code EGAS00001005173.
All ST data from this study is available from the Zenodo data repository (DOI: 10.5281/zenodo.4739739 - https://zenodo.org/record/4739739). ST data from the Andersson et al. study can be downloaded from the Zenodo data repository (DOI: 10.5281/zenodo.3957257 - https://zenodo.org/record/4751624#.Yw06i3ZByMI). For deconvolution of Visium data, please see the stereoscope method at https://github.com/almaan/stereoscope from the Andersson et al (2020) study. https://www.nature.com/articles/s42003-020-01247-y See this issue thread for a discussion on how to load the spatial data from Zenodo into Seurat.
All other relevant data and analysis are available from the authors upon request. For further enquires, please either raise an issue via GitHub or email John Reeves (Data Manager - j.reeves(at)garvan.org.au), Sunny Wu (Lead Author - s.wu(at)garvan.org.au) or Alexander Swarbrick (Lab Head - a.swarbrick(at)garvan.org.au).