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README.md

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Instructions for Data Download

Before you repeat the analysis, please read the following instructions carefully to create the data folder and download the data. Please note that all the data is for research purposes only.

The data folder should contains the following subfolders:

  1. TNBC_scRNA_GSE169246 folder: preprocessed single cell RNA-seq (scRNA-seq) data for TNBC patients, which is downloaded from GSE169246 and preprocessed with Fig1.script1_Preprocess_scRNAseq.R. We provide the preprocessed data through the zenodo (Version v1.1.1.0-1) DOI. Please download and decompress the data to the data/ folder, rename the downloaded folder to TNBC_scRNA_GSE169246. The path to the data should be data/TNBC_scRNA_GSE169246/*.rda.

  2. bulk_transcriptomics folder: preprocessed bulk transcriptomics data for pan-cancer patients.

    There are three ways to download the data:

    • We provide the data source for each dataset in supplementary table 4 of the manuscript, including the original publication, assession number, and the link to the data source. You can download or request the data from the original publication. And preprocess the data according to this example.
    • We provide preprocessed GEO datasets in the zenodo (Version v1.1.1.0-2) DOI. These datasets are used in the manuscript and can be used as an example to repeat the analysis.
    • We deposited all the preprocessed data in the zenodo (Version v1.1.0.0) DOI. These datasets have restricted access and can be only used for the replication of the analysis in the manuscript. Please contact the corresponding author for more information. No other usage than repeat Fig.2 is allowed wihout permission.

    After you download or preprocessed the datasets, please save the data or rename the folder as bulk_transcriptomics. The path to the data should be data/bulk_transcriptomics/*.rda.

    In addition to this preprocessed data, this repository also contains the intermediate and result files generated with TimiGP-Response. If you want to explore the immune landscape assocaited with the response to immunotherapy, you can use the intermediate files in the Fig2 folder. Please refer to the README for more information.

    Note: The data file name is a little different from what displayed in our manuscript. The config file provide the mapping between the data file name ("oldname") and the dataset name in the manuscript ("newname"), and the location to the TimiGP-response result folder.

  3. TNBC_IMC_zenodo.7990870 folder: preprocessed image mass cytometry (IMC) data for TNBC patients, which is downloaded from zenodo. Please request the data from the original publication. Once you have the data, please rename the downloaded folder as TNBC_IMC_zenodo.7990870 and save it to the data folder. The path to the data should be data/TNBC_IMC_zenodo.7990870/.