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.

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Crag Map

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

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Building a Beginner Trad Rack

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.

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Variant Filtering and QC

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.

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Overlapping Genomic Regions of Interest

Overlapping Genomic Regions of Interest

This is a quick tutorial on finding genes near candidate SNPs using my favorite R package plyranges.

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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)

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