Software

Genetic association studies

Code for fitting an ultra-sparse variational Bayes spike regression model, with applications to Genome-wide association studies (vBsr) is here. WARNING: Code is in an early release form (version 0.0.1), and details of the model are forthcoming.
Code for approximate power calculations for identification of gene x gene and gene x environment interactions in genomewide association studies using a two-stage analysis. Download the package powerGWASinteraction from CRAN.
- This method is described in C. Kooperberg and M. LeBlanc (2008). Increasing the power of identifying gene x gene interactions in genome-wide association studies Genetic Epidemiology, 32, 255-263.
Code for SNP-Haplotype Adaptive Regression (SHARE) to perform multi-locus analysis in order to account for LD patterns observed in human genome developed by James Dai is available in the package SHARE from CRAN.
- This method is described in J. Y. Dai, M. LeBlanc, N. L. Smith, B. Psaty and C. Kooperberg (2009). SHARe: an algorithm to select the most informative set of SNPs for candidate genetic association. Biostatistics, 10, 680-693.
Code for semiparametric estimation exploiting covariate independence in two-phase randomized trials developed by James Dai is available in the package TwoPhaseInd from CRAN.
- This method is described in J. Y. Dai, M. LeBlanc, and C. Kooperberg (2009). Semiparametric estimation exploiting covariate independence in two-phase randomized trials. Biometrics, 65, 178-187.

Logic Regression
Logic Regression: R libraries to fit logic regression models.

The Logic regression program is described in Ingo Ruczinski, Charles Kooperberg, and Michael L. LeBlanc (2003). Logic Regression. Journal of Computational and Graphical Statistics, 12, 475-511.
Extensions are discussed in Charles Kooperberg and Ingo Ruczinski. Identifying interacting SNPs using Monte Carlo Logic Regression. Genetic Epidemiology, 28 , 157-170.

Improved background correction for spotted DNA microarrays is implemented in Gordon Smyth: R code. It is also implemented in Gordon Smyth's Limma package on bioconductor as the function kooperberg.
- This method is described in C. Kooperberg, T. G. Fazzio, J. J. Delrow, and T. Tskuiyama (2002) Improved background correction for spotted DNA microarrays Journal of Computational Biology, 9, 55-66.

Software for hare, heft, lspec, logspline, polyclass and polymars, as well as the logspline version discussed in Stone et al (1997) are now available as an R-package. You can download the package polspline from CRAN. (Version 1.0.11, 5/24/2005.)
Software for logspline as well as the logspline version discussed in Stone et al (1997) are now available as an R-package. You can download the package logspline from CRAN. (Version 2,9,2, 4/18/2005.) The latest version of logspline is always part of the latest version of polspline.