Software
We have developed a variety of software that have been used for genetic, genomic and more generally, biomedical research. We have programs that are broadly distributed, have broad academic, research and commercial uses and perform reliably and precisely according to the computing demands of end-users. Additionally, we have programs that need more work and testing and others that are fully developed. Below are the programs th at we have developed with a brief description of each:
AAOT — Association Analysis of an Ordinal Trait
This is an SAS program that converts an ordinal trait to a quantitative trait, and prepares a data set that can be fed into FBAT for association analysis.
CTMBR — Classfication Trees for Multiple Binary Responses
This is a program to construct classification trees for multiple binary responses. In Biomedical Research, many diagnoses are based on multiple items such as depression and anxiety. This program makes it possible to conduct analysis at the item level.
HapForest — Forest for Detecting Haplotypes and Interactions among Them in Association with a Disease
This program implements a forest-based approach to accommodate the haplotype uncertainties and variable importance to sort out significant haplotypes and their interactions in genomewide case-control association studies.
LOT - Linkage Analysis of Ordinal Traits
This program performs linkage analysis of ordinal traits for pedigree data. It implements a latent-variable proportional-odds logistic model that relates inheritance patterns to the distribution of the ordinal trait.
MASAL — Multivariate Adaptive Splines for Analysis of Longitudinal Data
This C program takes a data structure similar to that of "CTMBR", except that there is a time variable "t".
RTREE — Classification Trees for Risk Profile and Diagnosis
Program that analyzes relative risk and conducts sib pair linkage analysis using tree-based methods. This program can be executed to automatically generate a tree structure or allow the user to construct a tree of his or her choice.
STREE — Survival Analysis Trees
Represents one of the most popular uses of tree-based methods. This program identifies prognostic factors that are predictive of survival outcome and time to an event of interest. It partitions a study sample into strata to reveal distinct patt erns of survival among subgroups.
Twin Analysis — Twin Analysis Using SAS
This program uses SAS PROC NLMIXED and PROC MIXED to conduct twin analysis to estimate heritability of binary and quantitative traits.
Willows
This is a software package that includes three classifiers: classification tree, random forest, and deterministic forest. This package is built on RTREE mainly to implement the most efficient memory use for SNP data.
