Software and Publications for Genetics with R/S-PLUS

Please send URL of your R software, and I am more than happy to include it here.

SOFTWARE (CRAN task view for genetics and




  • Joo J, Kwak, M, Zheng G. Improving power for testing genetic association in case-control studies by reducing the alternative space. Biometrics 2010; 66:266-276
  • Wakefield J. Bayesian Methods for Examining Hardy-Weinberg Equilibrium. Biometrics 2010; 66:257-65
  • Wakefield J. Bayes Factors for Genome-Wide Association Studies: Comparison with P-values.Genet Epidemiol 2009;33:79-86
  • Holden et al. GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics 2009;24:2784-5
  • Kitamura, et al. Programs for calculating the statistical powers of detecting susceptibility genes in case-control studies based on multistage designs. Bioinformatics 2009;25:272-3
  • Foulkes AS. Applied Statistical Genetics with R for Population-based Association Studies. Springer 2009
  • Guillot G, Santos F, Estoup A. Analysing georeferenced population genetics data with Greenland: a new algorithm to deal with null allles and a friendly graphical user interface. Bioinformatics 2008;24:1406-7
  • Jombart T.adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 2008;24:1403-5
  • Siegmund D, B Yakir. The Statistics of Gene Mapping. Springer 2007
  • Wu R, C-X Ma, G Casella.Statistical Genetics of Quantitative Traits-Linkage, Maps and QTL. Springer 2007
  • Rezvoy C, Charif D, Gueguen L, Marais GAB. MareyMap: an R-based tool with graphical interface for estimating recombination rates. Bioinformatics 2007;23:2186-9
  • Yandell BS, Mehta T, Banerjee S, Shriner D, Venkataraman R, Moon JY, Neely WW, Wu H, Smith R, Yi N. R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. Bioinformatics 2007; 23(5):641-643
  • Kooperberg C, M LeBlanc. Increasing the power of identifying gene x gene interactions in genome-wide association studies. Genet Epidemiol 2008;32:255-63
  • Zhao JH. gap: genetic analysis package. J Statist Soft 2007; 23(8):1-18
  • Sun S, CMT Greeenwood, RM Neal. Haplotype inference using a Bayesian hidden Markov model. Genet Epidemiol 2007;31:937-48
  • Clayton D., Leung,H.T. An R package for analysis of whole-genome association studies. Hum Hered 2007; 64:45-51
  • Aulchenko YS, Ripke S, Isaacs A, van Duijn CM (2007). GenABEL: An R Library for genome-wide association analysis. Bioinformatics 2007; 23(10):1294-6
  • Gonzalez,J.R., Armengol,L., Sole,X., Guino,E., Mercader,J.M., Estivill,X., Moreno,V. SNPassoc: an R package to perform whole genome association studies. Bioinformatics 2007; 23: 644-645 areast-language: ZH-CN; mso-bidi-language: AR-SA”}
  • Shin J-H, McNeney B, Graham J. Case-control inference of interaction between genetic and nongenetic risk factors under assumptions on their distribution. Statist Appl Genet Mol Biol 2007; 6(1):13
  • Estimating the null and the proportion of non-null effects in large-scale multiple comparisons. JASA 2006; 102:495-506
  • Hoffmann T, Lange C. P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R. Bioinformatics 2006; 22(24):3103-5
  • Shin J-H, Blay S, McNeney B, Graham J. LDheatmap: An R function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms. J Statist Soft 2006; 16 (3):1-9
  • Burkett K, Graham J, McNeney B. happassoc: software for likelihood inference of trait associations with SNP haplotype and other attributes. J Statist Soft 2006; 16(2):1-19
  • Zhao JH, Tan Q. Genetic dissection of complex traits in silico: approaches, problems and solutions. Current  Bioinformatics 2006; 1(3):359-69
  • Tan H, M Coram, P Wang, X Zhu, N Risch. Reconstructing genetic ancestry blocks in admixed individuals. Am J Hum Genet 2006; 79:1-12
  • Zhao JH, Tan Q. Integrated analysis of genetic data with R.Hum Genomics. 2006 Jan;2(4):258-65
  • Tufto J, Cavallini P. Should wildlife biologists use free software? Wildlife Biology 2005; 11(1):67-76
  • Gentleman R, V Carey, W Huber, R Irizarry, S Dudoit. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer 2005


  • Zhao JH, Luan JA, Tan Q, Loos R, Wareham N. Analysis of Large Genomic Data in Silico: The EPIC-Norfolk Study of Obesity. Huang, D.-S., Heutte, L., and Loog, M. Communication in Computer and Information System [2], 781-790. 2007.  Springer-Verlag Berlin Heidelberg
  • Saxton AM. (Ed) Genetic Analysis of Complex Traits Using SAS. 2004, SAS Publications  ISBN:  1-59047-507-0 (#154)

Created 9/3/2006, Last changed 19/12/2018