mchizk1 / UA_Fruit_Breeding

This repository serves to document, share, and collaborate on scripts used in the University of Arkansas fruit breeding lab.

UA_Fruit_Breeding

UA Blackberry GWAS Project

• See the markdown for documentation of the project thus far! Or see the code below.
• readVCF_ARonly.R - This is a script for filtering the 8.7 Gb VCF file from RAPiD Genomics
• Dogify.R - Making tetraploid incremental SNP calls in updog and formatting for GWASpoly.

GST4 Muscadine Validation Project

• See the markdown for documentation.

Miscellaneous R

• QRlist.R - Generates a list of QR codes for the Fieldbook App with additional descriptive plot info
• BLUP.R - Estimating Best Linear Unbiased Predictions (BLUPs) in R with lme4 for phenotypic GWAS data

Miscellaneous SAS

• BLUPs.sas - Estimating Best Linear Unbiased Predictions (BLUPs) in SAS for phenotypic GWAS data
• MultiMixed.sas - A handy SAS macro for running PROC MIXED over multiple traits with fewer lines of code

Other Scripts

• Vibration_Table.ino - This is an Arduino script used to estimate frequency and displacement from tachometer and accelerometer data. A big thanks to Randy Andress in Biological and Agricultural Engineering for writing this for us.
• BKB_IJ.ijm - An ImageJ macro script that standardizes white-balance, estimates RDR, and counts drupelet number.