Matthew Stephens Lab Division of Human Genetics Department of Statistics University of Chicago Program Multi-SNP evaluation for Genetic Association Reports, via Bayesian Variable Selection Regression The software programs piMASS (Posterior inference implementing Design Averaging and Subset Choice),
Windows 7 Pro Key, published and taken care of by Yongtao Guan, implements MCMC-based inference options for Bayesian variable-selection regression described in Guan and Stephens (2011) This program was produced to complete multi-SNP association evaluation for substantial (genome-wide) datasets, although it could possibly also be applied to scaled-down association analysis information (e.g. candidate genes or regions), and in this situation it varieties an substitute towards the multi-SNP association evaluation capabilities of BIMBAM (under). It might also be useful for Bayesian variable selection regression in large-scale difficulties a great deal more typically. Sparse Issue Evaluation (SFA) This program employs ECME to compute a sparse, low-rank matrix factorization for any provided matrix, as described in:Engelhardt BE, Stephens M (2010) "Analysis of population structure: a unifying framework and novel practices based mostly on sparse aspect evaluation." PLoS Genetics 6(9):e1001117.Download C++ code and instructions for SFA 1.0 and further documentation for the SFA model.BIMBAM: computer software for Bayesian IMputation-Based Association Mapping. The program BIMBAM implements approaches for assocation mapping, based mostly on those described in Servin, B and Stephens, M (2007). Imputation-based evaluation of association scientific tests: candidate genes and quantitative traits. PLoS Genetics, 2007. BIMBAM can handle both massive association research (e.g., genome scans) and more compact reports of candidate genes/regions. The application is distributed under the GNU Public License (GPL). To register and download, click here. Instructions are available here fastPHASE: software system for haplotype reconstruction, and estimating missing genotypes from population data The program fastPHASE implements systems described in Scheet, P and Stephens, M (2006). A fast and flexible statistical design for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet fastPHASE can handle larger data-sets than PHASE (e.g., hundreds of thousands of markers in thousands of individuals), but does not provide estimates of recombination rates. Our experiments suggest that haplotype estimates are slightly less accurate than from PHASE, but missing genotype estimates appear to be similar or even slightly better than PHASE. The software is free for non-commercial use, and might possibly be licensed for commercial use. To view the terms and conditions, and then proceed to download, click here. PHASE: application for haplotype reconstruction, and recombination rate estimation from population info The program PHASE implements strategies for estimating haplotypes from population genotype info described in Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian ways for haplotype reconstruction from population genotype info. American Journal of Human Genetics, 73:1162-1169. Stephens, M., Smith, N., and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics,
Microsoft Office 2010 Standard Key, 68, 978--989. Stephens, M., and Scheet, P. (2005). Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation. American Journal of Human Genetics, 76:449-462. The computer software also incorporates options for estimating recombination rates, and identifying recombination hotspots: Crawford et al (2004). Evidence for substantial fine-scale variation in recombination rates across the human genome. Nature Genetics,. The software is free for non-commercial use, and could be licensed for commercial use. To view the terms and conditions, and then proceed to download, click here. Instructions for PHASE are included on the download site,
Windows 7 64bit Key, or are also available here. SCAT: Smoothed and Continuous AssignmenTs The program SCAT (Smoothed and Continuous AssignmenTs) implements a Bayesian statistical method for estimating allele frequencies and assigning samples of unknown (or known) origin across a continuous range of locations, based mostly on genotypes collected at distinct sampling locations. In brief, the idea is to assume that allele frequencies vary smoothly in the study region,
Windows 7 Home Basic 32bit, so allele frequencies are estimated at any presented location utilizing observed genotypes at near-by sampling locations, with info at the nearest sampling locations being offered greatest weight. Details are offered in S K Wasser, A M Shedlock, K Comstock, E A Ostrander, B Mutayoba, and M Stephens. Assigning African elephant DNA to geographic region of origin: applications to the ivory trade. Proc Natl Acad Sci U S A,
Office 2007 Activation Key, 41:14844-14852, 2004. SCAT is available here. HOTSPOTTER: software package for identifying recombination hotspots from population SNP information This application by Na Li implements practices from:
N Li and M Stephens. Modeling linkage disequilibrium and identifying recombination hotspots making use of single-nucleotide polymorphism information. Genetics, 165(4)2213-2233, 2003. It is available free from here. Please direct comments and questions regarding HOTSPOTTER to Na Li, at wuolong SPAMBLOCKER AT gmail.com
Windows 7 Pro Key Stephens Lab
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