The following folders/files are part of this repository: Zip-Archive "MelanomaIMC-Zenodo": contains all code that is available as Github release Folder "analysis": contains all .rmd files that are required to generate the SingleCellExperiment object with single-cell data required to reproduce all figures Folder "code": contains all helper functions required for the analysis pipeline Folder "celltype_classifier": contains scripts to load all images and masks to start the cytomapper Shiny application to generate labeled data for the random forest classifier Folder "helper_functions": all R helper functions (such as patch/milieu detection, etc) Folder "data": empty, store data folders here ("data_for_analysis" and "full_data") Folder "docs": all .html files generated from the scripts stored in the "analysis" folder. Contains also all panels from the figures as .pdf or .png Folder "output": empty Zip-Archive "data_for_analysis": contains processed data such as SingleCellExperiment objects, clinical data tables, labeled data for the random forest classifier, etc Folder "12plex_validation": data used to validate the RNAScope 12-plex system Folder "ClustalW_results": data used to generate Fig S6G (Sequence similarity of RNAScope targets) Folder "protein": all data for the Protein data set (single-cell expression data, channel order, labeled data for the random forest classifier, clinical data table, etc) Folder "rna": same as protein folder but for the RNA&Protein data set Folder "scRNAseq": scRNA-seq data required to generate Fig. S7A Files "sce_*.rds": R objects containing the SingleCellExperiment container with all single-cell data and metadata, used for all R analyses. File "HPA_rna_celline.tsv": data used to generate Fig. S3B, bulk RNA seq data from cell-lines, Human Protein Atlas

This deposit contains data and code required to reproduce figures / supplementary figures of the article.