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| Bagphenotype | Mapping QTLs in populations descended from known founders [Note: this is legacy code and no longer maintained.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 |
| bmediatR | Bayesian model selection approach to mediation analysis. | article github |
| 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 |
| TIMBR | R package for inferring an allelic series of haplotype effects | github 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). | github article |