scleroderma

Python analysis package for somatic mutations and clonal hematopoiesis (CHIP) in blood exome sequencing from a systemic sclerosis cohort. Runs on ANNOVAR-annotated Mutect2 calls and covers mutation burden, CHIP prevalence and clinical associations, mutational signatures and GWAS convergence.

SSc skin yields six times fewer fibroblast nuclei than healthy skin in GSE312129, a composition confound for any between-group claim from that dataset.

Code behind "A pre-specified mineralization-inhibitor score separates systemic sclerosis fibroblasts within one study and does not replicate in an independent series." Byte-identical to the files that ran. Paper: 10.5281/zenodo.24026978