Software & Resources

Software

Note: this page was recently migrated from another server (owing to an institution-wide change in service provision) and so some links may not work. These are slowly being fixed but please contact william.valdar@unc.edu if you need something more quickly.

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Bagphenotype Mapping QTLs in populations descended from known founders [Note: this is legacy code and no longer maintained.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
website
Bagpipe Mapping QTLs in populations descended from known founders website
BayesDiallel An R package for Bayesian analysis of diallel crosses of inbred strains article
website
Diploffect Bayesian modeling of haplotype effects in multiparent populations. article
github
FReMA LASSO-based fractional resample model averaging, useful for reprioritizing SNP associations at GWAS loci (successor to LLARRMA) article
website
ISVdb Inbred Strain Variant Database: A repository for probabilistically informed sequence differences among the Collaborative Cross strains and their founders article
database
LLARRMA LASSO-based resample model averaging, useful for reprioritizing genetic associations in GWAS hit regions article
website
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
(errata)
website
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
article

Resources