By Dale R Nyholt
- The following webtools were developed during my time at the QIMR Berghofer Medical Research Institute (QIMRB).
- SECA to perform SNP effect concordance analysis using genome-wide association study (GWAS) summary results (Nyholt 2014), and the related
- iSECA to perform SECA using GWAS summary results for pre-prepared independent SNPs, and
- tutorial on performing LD clumping using the PLINK program (Purcell et al 2007) to prepare iSECA input.
- ZygProb web interface and access other details related to twin pair (Nyholt 2006).
- SNPSpD method of correcting for non-independence of SNPs in LD with each other (Nyholt 2004).
- matSpD to estimate the equivalent number of independent variables for a correlation (r) matrix.
- ssSNPer to identify statistically similar SNPs (ssSNPs) in the HapMap (Nyholt 2006).
- SECA to perform SNP effect concordance analysis using genome-wide association study (GWAS) summary results (Nyholt 2014), and the related
- Unfortunately, the web server on which the above run has been decommissioned and QIMRB is no longer able to support the above webtools.
- Note: links to non-functional cached versions of the above webtool pages are from the Internet Archive.
- Therefore, and given the cached webtool pages are not functional, I provide the following resources to allow users to set up a local version of the two tools still in common use:
- SECA (/iSECA),
- LD clumping tutorial, and
- matSpD (allowing an SNPSpD analysis).
- Download my novel software (LOD2P) to allow easy conversion of the most common LOD scores to P-values (Nyholt 2000)
- Download a copy of my MS Excel worksheet (relating to Nyholt 2006) enabling easy calculation of exact Random Match Probabilities from allele frequency data, for markers in unrelated and full sibling (DZ) pairs.
- Download a copy of my MS Excel worksheet (relating to Nyholt 2006) enabling easy calculation of approximate Random Match Probabilities from heterozygosities, for markers in full sibling (DZ) pairs.