I have set up this repository as a catch-all for the notes I make as I learn new programs and design pipelines. My Tutorials will focus on the codes I have used successfully with notes about what needed troubleshooting. I have attempted to make these walkthorughs clear and accurate with helpful details not included in the available vignettes.
- ADMIXTURE - used to estimate global genetic ancestry; walkthrough of a supervised admixed run on African Americans
- BASH Commands - navigating the server; basic bash commands for navigation, finding and viewing data; also detaching screens for backgrounf processes
- GENESES_PCRelate - used to estimate relatedness measurements in sample; genetic relatedness matrix generation
- GRM Methods Comparison - evaluates Pro's and Con's of 3 common GRM computation programs (GENESIS, REAP, GCTA) and conlcudes that GENESIS is the most robust for admixed populations
- Markdown - quick summary of markdown syntax used to create the following files
- PLINK_QC - intro to running quality control for genotype array data in PLINK to prepare for GWAS; example shown is the process used for the telomere project
- Useful_databases - a dynamic and curated list for different bioinfomatic databases by data type / research question
- ggplot_manhattan - function for creating a beautiful and customizable manhattan plot using ggplot2
See the Wiki tab for more details and tutorials.