Code used to produce the final figures and tables of the study "Spatial Transcriptomics in Breast Cancer Reveals Tumour Microenvironment-Driven Drug Responses and Clonal Therapeutic Heterogeneity".
Use the git clone command to create a local copy:
git clone https://github.com/cnio-bu/breast-bcspatial
You need to download additional data folders from Zenodo (DOI: 10.5281/zenodo.10638906) for the code to be functional:
-
visium/
: Contains processed spatial transcriptomics Seurat objects with deconvoluted spots, SCTransform-normalised counts, and clonal composition predicted with SCEVAN [1]. Please make sure to merge the contents of this folder with thedata/visium/scalefactors
folder that is provided in this repository. -
single-cell/
: Contains raw and filtered merged single-cell RNA-seq Seurat objects with unnormalised counts used as a reference for spot deconvolution. -
beyondcell/sensitivity
: Contains Beyondcell sensitivity objects with prediction scores for all drug response signatures in SSc breast. -
beyondcell/functional
: Contains Beyondcell functional objects with enrichment scores for all functional signatures.
These objects were generated with the code available at cnio-bu/ST-preprocess.
References
- De Falco A, Caruso F, Su X-D, Iavarone A, Ceccarelli M. A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data. Nat Commun. 2023;14:1074.
Once all data is downloaded, just run the code in the scripts/
folder in order. Then, run the code in the scripts/figures_and_tables
folder to generate the final figures and tables.
- María José Jiménez-Santos
If you have any questions, feel free to submit an issue.