Searching the GWAS Catalog and Calculating PRS
I search for my genomic variants in the GWAS catalog looking for variant-phenotype associations and calculate polygenic risk scores.
Annotating My Genomic Variants
I search my whole genome sequence data for any variants known to disrupt protein function or play a role in disease.
Crag Map
An interactive map tracking the locations of crags I’ve climbed at. Built with R shiny. Git Repo: joemcgirr/rock_climbing/crag_maps
Exercise Routine Generator
R Shiny app to create exercise routines based on desired training type, 3 rep max weight, and target muscle groups. Git Repo: joemcgirr/fitness_app
Building a beginner trad rack
A set of analyses I used to find the perfect combination of rock climbing gear. I collected data for trad equipment offered by several manufacturers to compare price/quality tradeoffs.
Variant Filtering and QC
This is a pipeline to generate a filtered SNP .vcf file from raw .fastq files. The approach is designed for hundreds of whole-genome low coverage sequences.
Grad School Advice
My thoughts on choosing a PhD program and thesis lab. Questions to ask before decide.
Overlapping Genomic Regions of Interest
This is a quick tutorial on finding genes near candidate SNPs using my favorite R package plyranges.
Using the FARM Computer Cluster
A tutorial on how to submit jobs on the UC Davis FARM cluster. Developed for ECL243 (Ecological Genomics graduate level course)