Software & Resources


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Name Description More info
Bagphenotype Mapping QTLs in populations descended from known founders [Note: this is legacy code and no longer maintained. For single locus mapping use BAGPIPE] article
Bagpipe Mapping QTLs in populations descended from known founders website
BayesDiallel An R package for Bayesian analysis of diallel crosses of inbred strains article
Diploffect Bayesian modeling of haplotype effects in multiparent populations. article
FReMA LASSO-based fractional resample model averaging, useful for reprioritizing SNP associations at GWAS loci (successor to LLARRMA) article
ISVdb Inbred Strain Variant Database: A repository for probabilistically informed sequence differences among the Collaborative Cross strains and their founders article
LLARRMA LASSO-based resample model averaging, useful for reprioritizing genetic associations in GWAS hit regions article
miqtl QTL mapping utilities for multiparent populations, both for haplotype association and SNP association. github
mvGWAS Tools for conducting genome-wide association studies that accommodate and target effects on phenotype variance github
Prephappy Preparation of input files for HAPPY website
Scorecons Scoring residue conservation from a multiple sequence alignment article
vqtl Mean-Variance QTL mapping: genome scans to accommodate and target genetic and non-genetic effects on trait variance in test crosses (eg, F2, backcross, etc). cran