tobyjohnson/gtx: Genetics ToolboX

Assorted tools for genetic and pharmacogenetic association analyses. The current focus is on tools that operate in an environment where genetic data and summary statistics are available via SQL queries against a database. There are also functions for simplifying and standardising pharmacogenetic analysis and reporting. There are (legacy) functions to support multi-SNP risk score analyses, multi-SNP conditional regression analyses, and multi-phenotype analyses, using summary statistics instead of using subject-specific data. There are (legacy) helper functions for reading and manipulating subject-specific genotype data, which provide a platform for calculating the summary statistics, or for using R to conduct other analyses not supported by specific GWAS analysis tools.

install.packages("remotes")
remotes::install_github("tobyjohnson/gtx")