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.