Spatial deconvolution of HER2-positive Breast cancer delineates tumor-associated cell type interactions

Processed count matrices, brightfield HE-images (plain and annotated), spot selection files and meta-data associated with the manuscript "Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships".

The content of the files are:

count-matrices.zip - processed count matrices formatted as [n_spots]x[n_genes] and named as [PATIENT][SECTION].tsv.gz. 

images.zip - contains two folders HE and annotation, the former holds the HE-images for respective section named as [PATIENT][SECTION].jpg, the latter holds the annotated (by the pathologist) images named by patient (only one section from each patient was annotated).

spot-selection.zip - contains .tsv files to map array coordinates to pixel coordinates, allowing the spots and their associated expression values to be visualized jointly. Files are named as [PATIENT][SECTION]_selection.tsv.gz

meta.zip - for all annotated sections, these files are similar to the spot-selection files, but also includes the label of each spot (e.g., breast glands, connective tissue, etc.).

All files are password protected (encrypted), use the passeword zNLXkYk3Q9znUseS do decrypt the data.

code.zip - a clone of the github repository created (2021-05-12).