Brian S. Yandell's Software Information

• R Software Introduction for Stat 571
• R Appendices for the Stat/For/Hort 571 Course Notes
• Graphical Data Presentation with Emphasis on Genetic Data (R code for ASHS paper)

  My Software Releases

• GCVPACK: Routines for Generalized Cross Validation (free release in 1986; now part of base of R; Bates, Lindstrom, Wahba and Yandell 1987)
• MCMC-QTL: Markov chain Monte Carlo inference for Quantitative Trait Loci. (free release in 1998; Satagopan, Yandell, Newton and Osborn 1996).
• RevJump-QTL: Bayesian model Determination of the Number of QTLs using Reversible Jump MCMC. (free release in 1999; Satagopan and Yandell 1998).
• Splus/QDA: Quality Data Attributes Analysis. (proprietary release in 1999; Yandell and Tragon Corporation).
• Practical Data Analsysis: library(pda) for Splus and R. (free release in 1997; revised in 2000)
• Microarray Data Analysis: library(pickgene) for R. (free release in 2001; Lin et al. 2001; CRAN in 2003)
• Quantitative Population Ethology: library(ewing for R. (free release in 2001; Ewing et al. 2001)
• Bmapqtl: Bayesian QTL mapping module for QTL Cartographer. (public domain release in 2001; Gaffney 2001)
• R/bim: Bayesian interval mapping R library. (free release in 2002; CRAN in 2003; Bioconductor in 2004.
• R/qtlbim: QTL Bayesian Interval Mapping. Improved and totally revamped R library for model selection with Bayesan interval mapping, allowing for covariates and epistasis; CRAN in 2006.
• R/qdg: QTL-driven dependent graphs R library (CRAN 2008); See Chaibub Neto E, Ferrara C, Attie AD, Yandell BS (2008) Inferring causal phenotype networks from segregating populations. Genetics 179 : 1089-1100. [doi:10.1534/genetics.107.085167]