Various tools written in python to for HLA (human leukocyte antigen) analysis in genetics studies.
This supports HLA amino acids imputed using both SNP2HLA (old) and Michigan Imputation Server's HLA imputation (new) output format.
Analysis tools so far include, basic additive model, addition of clinical/environmental covariates, survival analysis and interaction (between alleles) analysis.
If there is interest in using the tools, feel free to clone the repository and install it by entering the corresponding directory containing the code via terminal and enter the following:
pip install .
Everything works so far (except plotting, that is work in progress) but could do with code refactoring.
If you need help using this or understanding HLA analysis, feel free to get in touch: chuanfu.yap@manchester.ac.uk