FOR PEER REVIEW: MR1-restricted T cell clonotypes are associated with 'resistance' to M.tuberculosis infection - original code

Tuberculosis is caused by <em>M. tuberculosis</em> (M.tb) and is the leading infectious killer worldwide, responsible for 1.5 million deaths annually. New treatments require a detailed understanding of the underlying protective immune mechanisms for this human-adapted pathogen. We recently reported on a unique cohort of household contacts that appear to ‘resist’ <em>M. tuberculosis</em> infection (Lu et al. Nature Medicine 2019). We showed that ‘resisters’ harbor IFN-γ independent functional profiles that may mediate protection. In this follow up study, we asked whether other T cell subsets might be associated with the ‘resister’ phenotype. Specifically, we focused on donor-unrestricted T cells that mediate recognition of non-peptide antigens, such as lipids and metabolites. In this repository, we include all R code required to recreate manuscript figures.