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This repository provides background, instructions, and an example of how to run the routine PGx analysis pipeline (gtx R package) in GSK's Global Data Center (GDC).

Analysis Pipeline Example

First time users should follow these instructions and run the example analysis as a test to ensure their compute environment has been setup correctly.

Analysis Pipeline Instructions

Once you have successfully run the example, you can follow these instructions to setup a real analysis.

Post Analysis Pipeline Instructions

Based on data and results from the analysis pipeline, this post analysis pipeline generates merged phenotype/genotype data, regional association plot, and phenotype by genotype association plot for variants of interest (specified by user).

Controlled Instance

This information is mostly for administrators but may be useful as a reference to users.

Supported Statistical Models

This page lists the current analysis types the pipeline supports.