PYPE

PYPE automates phenome-wide association studies (PheWASs) and Mendelian randomization (MR) analyses to discover genotype-phenotype relationships and potential causal links between traits in biobank-scale investigations.

Key Features:

• PheWAS Automation: PYPE utilizes input genotype or phenotype files to automatically estimate associations between chosen independent variables and phenotypes.
• Visualization Generation: PYPE produces a variety of visualizations for interpreting association results.
• Functional Annotation: PYPE identifies nearby genes and functional consequences of significant associations.
• Mendelian Randomization: PYPE identifies possible causal relationships between phenotypes using MR under a variety of causal effect modeling scenarios.

Scientific Applications:

• Pleiotropy Discovery: PYPE documents relationships between genotypes and multiple phenotypes to uncover unexplored genotype-phenotype associations.
• Causal Inference: PYPE makes causal statements about pairs of phenotypes by comparing their genetic architecture.

Methodology:

PYPE is implemented as a Python pipeline that processes input genotype or phenotype files to estimate associations and perform Mendelian randomization analyses.