Codes used in pan-cancer T cell study

• "TCellMap.R" is a tool we developed to automatically align and annotate T cells in a scRNA-seq dataset. It uniformly aligns T cells from the query dataset with the T cell maps that we built in our pan-cancer T cell study.

• The python script "Res_largerT.py" functions as a pipeline for the analysis and visualization of SRT data.

• The directories titled "fig1/2/3/4/5/6" contain additional scripts used for generating figures in the manuscript. Furthermore, the "data_preprocess" folder hosts scripts designed to preprocess raw data. Those scripts are used for tasks such as batch-correction and dimensional reduction, etc.