Codes for reproducing results of ICI repertoire paper (Aoki et al., 2022).
Code for processing data is "220210_ICIrepertoire_preprocess.ipynb." Code for plotting figure is "220210_ICIrepertoire_plotting.ipynb."
Raw data for single-cell RNAseq is stored in the directory "raw.data." Raw data for single-cell TCRseq is stored in the directory "scTCR_rawdata." Raw data for bulk TCRseq is stored in the directory "BulkTCR_rawdata."
Seurat object for creating figure is "Aoki_3rd_res0.6scTCRmerged.ABnt.AddSig.pseudotime.rda."
These codes are run in the Docker container haokimriid/singlecell Please install the docker image by the following command.
docker pull haokimriid/singlecell
Launch Jupyter from the Docker image and work on Jupyter. For, Windows10 Pro, run the following command.
docker run --rm -p 8888:8888 -v /mnt/your-working -directory/:/opt/work daisuke1121/immunogeneteqs jupyter notebook --allow-root
Then, Copy the http://127.0.0.1:8888/?token=~ part (URL) and launch it in your browser.