yewero / BrCa_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".

BrCa_cell_atlas

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.

Data Availability

processed & filtered scRNA-Seq data

All processed scRNA-seq data is available for in-browser exploration and download through the Broad Single-Cell portal at https://singlecell.broadinstitute.org/single_cell/study/SCP1039. Processed data is also available on GEO (GSE176078).

Raw scRNA-Seq data

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.

Spatial transcriptomics data

All ST data from this study is available from the Zenodo data repository (DOI: 10.5281/zenodo.4739739). ST data from the Andersson et al. study can be downloaded from the Zenodo data repository (DOI: 10.5281/zenodo.3957257). 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

Contacts

All other relevant data and analysis are available from the authors upon request. For further enquires, please email Alexander Swarbrick ([e-mail]) or Sunny Wu ([e-mail]).