Mitochondrial Transcription Factor A Regulates FOXP3+ T Cell Mediated Maintenance of CD4+ T Cell Landscapes and Immunological Aging
Data were collected after mapping all fastq files to the mm10 genome with the cellranger v6.0 software with default paramaters by using "cellranger count".
Please check the sessionInfo.txt in the script folder
run the run.r for clustering, cell annotation, differential expressed analysis and GSEA for all cell types. The metadata.csv and Embedding.csv in the data folder can be used to skip the integration, clustering analysis. The metadata.csv includes all cell information and the Embedding.csv includes UMAP and TSNE information.
run the cd4.r for the cd4 analysis. The cd4metadata.csv and cd4Embedding.csv in the data folder can be used to skip the integration, clustering analysis. The cd4metadata.csv includes all cell information and the cd4Embedding.csv includes UMAP and TSNE information.
run the cd4_traj.r, cd4_scenic.r and cd4_velo.r for all other analysis. The cd4_traj.rdata and cd4_scenic.rdata in the data folder are the results from Monocle and pySCEINIC packages.