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

<strong>- melanoma_IMC_data.zip</strong> 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 <strong>Melanoma_panel.csv</strong>. <strong>- Melanoma_code_data.zip</strong> The zip file contains the 4 folders described as follows: Folder ”data“: the processed data for the result shown in paper<br> - Folder "input": <br> - sc_data.csv: the single cell protein expression data;<br> - Folder "abundance": the cell type abundance files;<br> - Folder "clidata": the response and survival data for 4 melanoma datasets used in the paper; <br> - Folder "hc_result": TME archetypes annotation for each sample/ROI from hierarchical clustering;<br> - Folder "ICB": data for ICB analysis (presented in FigS3);<br> - Folder "meta": panel file for clustering;<br> - Folder "RNAseq_data": the RNAseq data for 4 melanoma datasets used in the paper;<br> - Folder "RNAseq_deconv": the result of cell type deconvolution from bulk RNAseq; <br> - Folder "spatial": data for neighbourhood analysis (presented in Fig3, FigS4).<br> - Folder "output": intermediate result for analysis. Folder "Rscript": R scripts for reproducing results in the paper.<br> - generate_Figs.Rmd: ploting figures presented in the paper;<br> - functions.R: functions used for analysis;<br> - Clustering.Rmd: determining cell types based on marker intensities;<br> - Spatial_analysis.Rmd: neighbourhood analysis to get significant interction/avoidance cell relationships. Folder "Figs": figures presented in paper. Folder "HE_figs": the H&amp;E image and the ROIs distribution for each sample.