rat_genomic_analysis

Quick Description

This is an analysis of the data from the Abe Palmer lab regarding the PTRS project and PhenomXcan. In the analysis, there are steps to download the data, format the data and run the scripts from the old PredictDB pipeline.

Data

The data can be found at this box file. The only files from this that I used is the 'genogex.Rdata' file and the raw count phenotype file.

Files

1. PalmerLab_Rat_Analysis.Rmd - this is where all of the steps that I went through and documented are. Most of it is data wrangling and running scripts from the scripts folder
2. Scripts folder - has all of the scripts which are individually documented as well as documented in the analysis.Rmd file described above. I would go through the .Rmd file first as it is explanatory.

Prediction models

Generated by Tyson (request access to Haky if needed) https://uchicago.box.com/s/u74s7owm0zyzpdqjbpmt0couugi6upxp