Liz Cooper's repositories
GWAS_Pipelines
Instructions and helpful R code for Running GEMMA and GAPIT
LDanalysis
A few simple scripts to calculate and plot LD using functions from the R genetics package
dadiScripts
A set of Python scripts for running migration models in dadi
formatConversion
A collection of Perl scripts to convert between various DNA sequencing and SNP data formats.
HapMap_Helpers
A set of Perl scripts to perform various functions with HapMap format SNP files
RILanalysis
R scripts for finding and plotting recombination breakpoints in a RIL population
SangerSeq_SNPCalling
Scripts and instructions for processing Sanger (ABI) sequence files
SAP_PlantGenome
A collection of scripts, command lines, and instructions for the analyses performed in "Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm"
CompGenWS
Data and scripts for Week 12 in class exercises
GenDivergence
Pipeline Instructions, Protocols, and Scripts used in "Genomics of Divergence-with-gene-flow in an Island Bird"
RAD_Pipeline_Info
Bioinformatics Pipeline for dRADseq Data
snpAnalysis
Perl scripts for the analysis of dRAD SNP data
BAP_Genetics
Scripts and Instructions for the analyses in "A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy"
compGenWS_112017
Scripts and Data for GEN-8900 class on 11-28-2017
eacooper400.github.io
Code to generate projects page
labProtocols
Various molecular lab protocols for DNA sequencing and library construction
pbs-scripts
User prologue and epilogue scripts for torque-based clusters
plumageColor
Files and Instructions associated with Monarcha pigmentation gene manuscript
QTL_GrainSorghum
Methods and Scripts for 2 QTL papers on Mapping Grain Quality Traits in Sorghum
sfsr
R package for analysing site frequency spectra (SFS)
startbootstrap-1-col-portfolio
A one column Bootstrap HTML portfolio template - created by Start Bootstrap