Code deposition for the paper: B Cells Promote CD4+ T Cell Immunosenescence and Aging Parameters

1. CellRanger_commands: Commands used for preprocessing single-cell transcriptomics fastq files.
2. B_T_scRNAseq_analysis.R: This R script performs 5’ single-cell transcriptomics, including VDJ T cell receptor analyses on splenic CD3+ cells from aged µMT and WT mice. The gene lists used for volcano plot are in the folder 'volcano_plot_genes'.
3. B2T_nichenet.R and T2B_nichenet.R: Those scripts utilizes the NicheNet framework to analyze B-to-T cell interactions, identifying ligand-receptor pairs that may mediate communication between these cells.
4. GeoMx_code_Spleen.rtf: Code for processing GeoMx data.