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 "<em>Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships</em>". The content of the files are: <strong>count-matrices.zip</strong> - processed count matrices formatted as [n_spots]x[n_genes] and named as [PATIENT][SECTION].tsv.gz. <strong>images.zip - </strong>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). <strong>spot-selection.zip - </strong>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 <strong>meta.zip - </strong>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 <em>zNLXkYk3Q9znUseS</em> do decrypt the data. <strong>code.zip </strong>- a clone of the github repository created (2021-05-12).