Codes for the paper "Pan-cancer single-cell landscape of tumor-infiltrating T cells"

Data and scripts for our paper titled "Pan-Cancer Single Cell Landscape of Tumor-Infiltrating T Cells".

Expression data

main expression data

* R objects of class `SingleCellExperiment`, contain expression data in mini-cluster level, annotations such as "meta.cluster" and "cancerType", and integrated harmony/UMAP. Each file for a dataset.
    file: data/expression/CD[48]/integration/int.CD[48].S35.sce.merged.rds

* R objects of class `SingleCellExperiment`, contain expression data in single-cell level and annotations such as "meta.cluster" and "miniCluster". The "miniCluster" column of the colData is linked to the colnames of the mini-cluster level `SingleCellExperiment` objects (int.CD[48].S35.sce.merged.rds).
    file: data/expression/CD[48]/byDataset/*.sce.rds

We also generated R objects containing only expression data from zhang-lab for convinence. 

* R objects of class `Seurat`, contain expression data in single-cell level and annotations such as "meta.cluster" and "cancerType", but integrated harmony/UMAP are not included. All data were newly generated by zhang-lab. 
    file: data/expression/CD[48]/integration/CD[48].thisStudy_10X.seu.rds

* R objects of class `SingleCellExperiment`, contain expression data in single-cell level. The meta-cluster annotation and integrated harmony/UMAP are not included. All data were generated by zhang-lab. Files:
    data/expression/zhangLab/S.10X.sce.rds    (newly generated data by 10x platform, solid tumor)
    data/expression/zhangLab/BCL.10X.sce.rds  (newly generated data by 10x platform, B-cell lymphoma)
    data/expression/zhangLab/MM.10X.sce.rds   (newly generated data by 10x platform, multiple myeloma)
    data/expression/zhangLab/S3.SS2.sce.rds   (data by SmartSeq2 platform, CHOL, CRC, HCC, and LUNG)

TCR data

* R object of class `data.table`, contain TCR data. Each line for a cell.
    file: data/tcr/byCell/tcr.zhangLab.comb.flt.rds

meta-information

* R object of class `"data.table`, contain meta-information. Columns include "patient", "loc", "dataset", "cancerType", "miniCluster", "meta.cluster" etc. Each line for a cell. 
    file: data/metaInfo/panC.freq.all.meta.tb.rds