1. CSig is a program for the test for association that incorporates information about deviation from Hardy-Weinberg proportions in cases.
Reference:
Wang J, Shete S. A test for genetic association that incorporates information about deviation from Hardy-Weinberg proportions in cases. Am J Hum Genet 83(1):53-63, 7/2008. e-Pub 6/2008. PMCID: PMC2443842.
2. OR_tilde.R is a R program for computing the corrected odds ratio for the association between genetic variants and secondary phenotype.
Reference:
Wang J, Shete S. Estimation of odds ratios of genetic variants for the secondary phenotypes associated with primary diseases. Genet Epidemiol 35(3):190-200, 4/2011. e-Pub 2/2011.
3. fxchrom package includes the Matlab program to perform association test for X-chromosomal genetic variant.
Reference:
Wang J, Yu R, Shete S. X-chromosome genetic association test accounting for X-inactivation, skewed X-inactivation, and escaping of X-inactivation. Genet Epidemiol 38(6):483-93, 9/2014.
Wang J, Shete S. Analysis of secondary phenotype involving the interactive effect of the secondary phenotype and genetic variants on the primary disease. Ann Hum Genet 76(6):484-99, 11/2012. e-Pub 8/2012.