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Liz Cooper's Projects

bap_genetics icon bap_genetics

Scripts and Instructions for the analyses in "A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy"

compgenws icon compgenws

Data and scripts for Week 12 in class exercises

dadiscripts icon dadiscripts

A set of Python scripts for running migration models in dadi

finches icon finches

Scripts and Instructions from "Genomic variation at the tips of the adaptive radiation of Darwin's finches"

formatconversion icon formatconversion

A collection of Perl scripts to convert between various DNA sequencing and SNP data formats.

gendivergence icon gendivergence

Pipeline Instructions, Protocols, and Scripts used in "Genomics of Divergence-with-gene-flow in an Island Bird"

hapmap_helpers icon hapmap_helpers

A set of Perl scripts to perform various functions with HapMap format SNP files

labprotocols icon labprotocols

Various molecular lab protocols for DNA sequencing and library construction

ldanalysis icon ldanalysis

A few simple scripts to calculate and plot LD using functions from the R genetics package

pbs-scripts icon pbs-scripts

User prologue and epilogue scripts for torque-based clusters

plumagecolor icon plumagecolor

Files and Instructions associated with Monarcha pigmentation gene manuscript

qtl_grainsorghum icon qtl_grainsorghum

Methods and Scripts for 2 QTL papers on Mapping Grain Quality Traits in Sorghum

rilanalysis icon rilanalysis

R scripts for finding and plotting recombination breakpoints in a RIL population

rio icon rio

Scripts and command lines used in the Rio comparative genomics and transcriptomics project

sap_plantgenome icon 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"

sfsr icon sfsr

R package for analysing site frequency spectra (SFS)

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