A Capstone Project for BYU BIO465
This repository hosts the project files and report for the BYU bioinformatics capstone. It's purpose is to provide a flexible pipeline to perform drug repositioning using GENIE and GDSC CNV data. It was developed by Jared Nielson, Richard Olpin and Kaleb Olson.
Of primary interest is the PipelineDevelopment.Rmd in which our pipeline which is written in a literate programming style.
Also of importance are the preprocessed .rds data files which allow you to avoid the cost of processing the data anew if you just want to play with the pipeline.
There are several exploratory .Rmd files that are here mainly for historical reasons.
The pipline was written in R and depends on the following libraries: ggplot2, viridis, dplyr, reshape2, magrittr, readr, synapseClient, tidyverse, and data.table
The recommended way to work with the pipeline is to simply load PipelineDevelopment.Rmd in RStudio.
The insight and guidence of Dr. Stephen R. Piccolo has been invaluable and without which this project would not have been possible.