💡 Cheng Lab at UC Davis



Our research interests are broadly involved in the development of statistical and computational methods for the (genetic) improvement of populations through more accurate, efficient, and biologically meaningful analysis. We have focused on the use of genomics, phenomics, pedigree, and other sources of big data in various species to better predict desired traits. These endeavours include

🚢 Projects


We on working on interesting projects! Click the dropdown menu to find more.

Details


🧮 Software Tools


$$Software\ Packages$$

<aside> 🧬 **JWAS**

</aside>

genotype  = get_genotypes("genotypes.csv")
pedigree  = get_pedigree("pedigree.csv")
model     = build_model("y = intercept + ID + genotype")
set_random(model,"ID",pedigree)
out       = runMCMC(model,phenotypes)

<aside> 🖥️ XSim

</aside>

#simulate sequence data and pedigree structures
build_genome(numChr,chrLength,nLoci,nQTL)
sires = sampleFounders(nfounders)
dams  = sampleFounders(nfounders)
sires1,dams1,gen1 = sampleRan(popSize, ngen, sires, dams)

<aside> 🔑 LPChoose

</aside>

#Optimizing Sequencing Resources in Genotyped Populations
LPChoose("data.csv",ninds)

$$Interactive\ Web\ Apps$$

<aside> <img src="https://img.icons8.com/ios/250/000000/linkedin.png" alt="https://img.icons8.com/ios/250/000000/linkedin.png" width="40px" /> ShinyJWAS

</aside>

<aside> 🍋 LMMonBoard

</aside>

<aside> <img src="data:image/jpeg;base64,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" alt="data:image/jpeg;base64,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" width="40px" /> Diagnostic Imaging

</aside>

Powered by Fruition