Gigabases to Gigabytes

Website and blog by an aspiring genome scientist

A site dedicated to my academic accomplishments and blog posts detailing my journey learning quantitative genetics, R, C++, and web development. I enjoy pondering questions in genomics and learning new statistical/CS/web techniques to enhance my research. "Computational biologists" have great opportunities to learn new skills, languages, and workflow practices to not only make their research easier, but incredibly fun. When not having fun with research and coding, I enjoy Seattle sports teams, good coffee, and good beer.

My hobbies and skills

Many of which I've developed during my time as a PhD student

  • Exploratory genomic data analysis
  • Literate programming for research
  • Software development with R & C++
  • Chemex and Aeropress brewing
  • Coding with my cat, Duchess
  • Drinking hoppy beer

Highlighted code and academic accomplishments

editTools

editTools is a fast R package designed using compiled code meant for the anlaysis of RNA editing from whole genome sequencing and RNAseq data. It is used to generate results for the manuscript Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements.

spin

spin is a simple R/Bash solution for easy submission of R scripts on PBS resource managers. Designed with literate programming and file organization in mind.

breedTools

breedTools is an R package that uses simple and fast methods to estimate breed or subpopulation composition. It is used to generate results for the manuscript Estimation of genome-wide and locus-specific breed composition in pigs.

My ePoster at the 2016 ISAG conference

An interactive ePoster showcasing swine editome patterns and its association with PRE-1 retrotransposons. During presentation, the ePoster was in presentation mode with click to advance set to off. Navigation is done using interactive ePoster elements.

BMC Genomics publication

Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements

T.A.S. publication

Estimation of genome-wide and locus-specific breed composition in pigs