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NEW: The first version (0.95) of HaplinGUI is now available under "Installation"

is a free software library written for the purpose of genetic association analyses of case-parent triad (trio) data and/or case-control data in candidate genes or a full GWAS. Haplin is implemented in the free statistical software R.
Haplin has its own web page here.

HaplinGUI is a graphical user interface to Haplin, which incorporates much of Haplin's functionality. HaplinGUI requires a separate installation, described under the
Installation tab.

* Figure created in HaplinGUI using Protovis

Some of the main features of Haplin are:
  • Analyses of the case-parent triad design, the case-control design, and "hybrid" designs using combinations of case-parent triads and control-parent triads.
  • Optimal use of designs with missing genotypic data, for instance a single SNP has not been typed for some individuals, or when the case father has not been genotyped at all, or when the control parents are not available.
  • Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data.
  • Estimation of relative risk (RR) associated with each haplotype, not only significance testing.
  • Optional estimation of effects of maternal haplotypes, particularly relevant in perinatal epidemiology.
  • Estimation of RRs, haplotypes etc. also on the X chromosome, with models including dose-response and X-inactivation.
  • Support for GWAS data and parallel processing.