Software & Data

QTLRel
http://github.com/pcarbo/QTLRel
QTLRel is an R package for mapping quantitative trait loci (QTLs) in experimental crosses such as advanced intercross lines (AILs) where relatedness among individuals should not be ignored.

QTLRel includes functions to estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for quantitative trait loci, and plot the mapping results.

breedail
http://github.com/pcarbo/breedail
R code to select breeders from an advanced intercross line so that they minimize inbreeding in the offspring.


lgsmfear
http://github.com/pcarbo/lgsmfear
Demonstration of QTL mapping for fear conditioning traits in LG/J x SM/J mouse advanced intercross line. Contains data and R to reproduce results of a forthcoming Genetics paper.

M. musculus Glo1 Duplication Genotyping Protocol