Hello, my name is Thomas Billman and I am an undergraduate Data Analyst for Dr. Ann Stapleton. This Github contains the code that I have written, files that I have analyzed, and output I have generated through the course of this job. The majority of my work has been done in RStudio, with some computing help from the supercomputer Stampede2 (formerly Stampede) which is maintained by TACC (Texas Advanced Computing Center).
The bulk of my work has been Variance Quantitative Trait Loci analysis. This is a technique which tries to find which specific genes effect an organisms measured phenotype. Usually these genes are close to one another, so we try to find clumps of genes that are all significant to the experiment. This usually involves hundreds or thousands of individuals, along with thousands of genes to analyze. As such, this is the type of analysis that typically involves the use of Stampede2. To the best of my knowledge, Stampede2 does not have any integrations with Github, so some of my files may not be present in this repository. The projects I have worked on so far include:
- Neighbor/Family
- Multiple Stress
- Spliced/Unspliced All of these projects have corresponding folders in this repository.
Also known as Quantitative Polymerase Chain Reaction. This is a molecular biology technique involving amplifying segments of DNA as part of confirming the identity of the plants in our experiment. All of the different qPCR analysis I have done can be found here.