Computer Programs
This page shows our main statistical genetics programs. The list will gradually be populated with my programs.
| GPM | A suite of programs for genotype pattern mining, i.e. evaluation of all pairs of genotypes and testing whether their frequencies differ in cases and controls. Users can apply these programs, or their own programs, to published datasets. |
| DNT | Based on genotype pairs obtained from GPM above, DNT finds SNPs significantly connected with other SNPs. |
| RunPM | A wrapper for pseudomarker, which combines linkage and association analysis and treats marker allele frequencies as nuisance parameters |
| L1outPRS | The L1outPRS program will create polygenic risk scores for different sets of best genetic variants. Results are cross-validated with the Leave-1-out method. See the manual at the link to Github, where you will also find the PRS program; it is analogous to L1outPRS but without cross-validation and works very fast. |
| Replic2 | Software for assessing significance of a replication GWAS dataset |
