Software Tools

• GENOSCORES a platform for calculating genotypic predictors of human traits
  Genoscores is a database of published genotype-phenotype associations from a large number of well-powered genome-wide association studies, including disease traits and biomarkers. The database is accompanied by an R package implementing score computation and downstream statistical analyses for cohorts with genotype (SNP) data.
• MRhevo: Bayesian Mendelian randomisation for inferring a causal effect of an exposure on an outcome using genetic markers as instrumental variables by marginalising over direct (pleiotropic) effects of the instruments on the outcome.
• nestedCV: Nested Cross-Validation with 'glmnet' and 'caret'.
• hsstan: Bayesian sparse prediction models using a hierarchical shrinkage prior distibution over model parameters implemented in Stan.
• GeneImp: fast imputation from ultra-low coverage sequencing
  GeneImp is an R package that implements genotype imputation to a dense reference panel given genotype likelihoods computed from ultra-low coverage DNA sequencing.
  We no longer maintain this software as there are now faster methods available for this task.