Hallmarks of T-cell exhaustion and antigen experience are absent in multiple myeloma from diagnosis to maintenance therapy

Code and data associated with Shasha et al., "Hallmarks of T-cell exhaustion and antigen experience are absent in multiple myeloma from diagnosis to maintenance therapy" (https://doi.org/10.1182/blood.2024025655). Description of files below: scRNA-seq_code.tar: Python notebooks for analysis of scRNA-seq data, including import and figure generation adata-rev.h5ad: processed CD8 T cell scRNA-seq data from all patients and samples combined. Includes condensed TCR info (refer to columns 'cdr3' for example; 'chain_id' was determined per batch and can be ignored) ics_tsv_repeat_dat.csv: ICS metadata cytof_ics_repeat_data.tar: normalized ICS tsv and fcs files from all patients and samples ics_repeat_analysis.R: R code for analysis of ICS data cytof_data.tar: CyTOF fcs and txt files (bead normalized and compensated, gated to CD8 T cells)