Multiplexed imaging mass cytometry reveals distinct tumor-immune microenvironments linked to immunotherapy responses in melanoma

- melanoma_IMC_data.zip The zip file contains the raw IMC images (in the raw_tiff folder) and corresponding single cell masks (in the mask folder) associated with the paper "Multiplexed imaging mass cytometry reveals distinct tumor-immune microenvironments linked to immunotherapy responses in melanoma". The MCD files by CyTOF IMC were exported to a multi-channel TIFF file including 41 channels, and the order of the channel was provided in the Melanoma_panel.csv. - Melanoma_code_data.zip The zip file contains the 4 folders described as follows: Folder ”data“: the processed data for the result shown in paper - Folder "input": - sc_data.csv: the single cell protein expression data; - Folder "abundance": the cell type abundance files; - Folder "clidata": the response and survival data for 4 melanoma datasets used in the paper; - Folder "hc_result": TME archetypes annotation for each sample/ROI from hierarchical clustering; - Folder "ICB": data for ICB analysis (presented in FigS3); - Folder "meta": panel file for clustering; - Folder "RNAseq_data": the RNAseq data for 4 melanoma datasets used in the paper; - Folder "RNAseq_deconv": the result of cell type deconvolution from bulk RNAseq; - Folder "spatial": data for neighbourhood analysis (presented in Fig3, FigS4). - Folder "output": intermediate result for analysis. Folder "Rscript": R scripts for reproducing results in the paper. - generate_Figs.Rmd: ploting figures presented in the paper; - functions.R: functions used for analysis; - Clustering.Rmd: determining cell types based on marker intensities; - Spatial_analysis.Rmd: neighbourhood analysis to get significant interction/avoidance cell relationships. Folder "Figs": figures presented in paper. Folder "HE_figs": the H&E image and the ROIs distribution for each sample