Software
All of the software is licensed under the GNU General Public License. Download and use of this software implies agreement to the terms in that license.
R/qtlMprob
Version 0.5 (29 Jan 2010)
Functions for both "reverse" and "full likelihood" approaches to binary trait mapping in experimental crosses with selective genotyping, as described in Manichaikul A, Broman KW (2009) Binary trait mapping in experimental crosses with selective genotyping. Genetics 182: 863-74 [Pubmed | Full Text | PDF]
The software is bundled as a package for R (aka Gnu S), an open-source implementation of the S language.
Associated R code to replicate analysis of Listeria data in Manichaikul and Broman (2009): [code]
R/pLODsims
Version 0.5 (23 July 2008)
Software for automated QTL model selection using penalized LOD scores. Model search is implemented to perform forward selection followed by backward elimination, and to report the best visited model according to user specified LOD penalties. Functions in this package were used to perform simulations presented in: Manichaikul A, Moon JY, Sen Ś, Yandell BS, Broman KW (2009) A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. Genetics 181: 1077-86 [Pubmed | Full Text | PDF]
The software is bundled as a package for R (aka Gnu S), an open-source implementation of the S language.
Associated code to replicate hypertension simulations from Manichaikul et al. (2009): [pLOD_L | pLOD_H | pLOD_a]
Associated code to replicate TgB simulations from Manichaikul et al. (2009): [pLOD_L | pLOD_H | pLOD_a]