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 www.bioconductor.org)

adegenet by T Jombart
BayesMendel
cnv-tools
dgc.genetics by D Clayton
Dprime by D Zaykin
EHP (Estimating haplotypes for pooled DNA sample)
GenABEL by Yurii Aulchenko
graphminer by Claudio Verzili
GSEA-SNP
Hap-Clustering by JY Tzeng
HAPLIN by HK Gjessing
HAPPY by R Mott
HapVLMC by SR Browning
HMM.hap by Shuying Sun
HWEBAYES by Jon Wakefield
LDGROUP by Takeuchi et al.
LINK/TDT by D Tritchler
MareyMap by Clement Rezvoy
multic by M de Andrade, E Lunde, E Atkinson
p_act by Michael Boehnke
Packages by B Devlin & K Roeder
Packages by D Schaid
Packages by K Broman
PedVizAPI
QTLBIM
SABER by H Tang Score statistics by K Wang
SNP-HWE by G Abecasis
Software by J Huang
Software by Jiashun Jin
Software by Charles Kooperberg
Software by Radford Neal
Software by Jon Wakefield
Softwareby P Kraft
Software from Leiden University Medical Center
Software from Statistical Source
Software by Muller-Myhsok
Software for two-stage design by J Satagopan
Software by Edwin JCG Van den Oord
TDTexact by R Betensky

STANDARD LINKS

PUBLICATIONS

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

SAS

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