Office 2007 License Stephens Lab

Matthew Stephens Lab Department of Human Genetics Department of Figures University of Chicago Software package Multi-SNP analysis for Genetic Association Studies, by way of Bayesian Variable Choice Regression The software programs piMASS (Posterior inference utilising Model Averaging and Subset Choice), created and taken care of by Yongtao Guan, implements MCMC-based inference practices for Bayesian variable-selection regression described in Guan and Stephens (2011) This application was formulated to accomplish multi-SNP association evaluation for huge (genome-wide) datasets, despite the fact that it could possibly also be applied to smaller sized association evaluation info (e.g. candidate genes or regions), and with this scenario it varieties an alternate to your multi-SNP association evaluation capabilities of BIMBAM (beneath). It could also be handy for Bayesian variable collection regression in large-scale troubles further generally. Sparse Factor Evaluation (SFA) This software program makes use of ECME to compute a sparse,microsoft Office 2010 Activation, 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 solutions based on sparse issue analysis." PLoS Genetics 6(9):e1001117.Download C++ code and instructions for SFA 1.0 and further documentation for the SFA design.BIMBAM: software programs for Bayesian IMputation-Based Association Mapping. The program BIMBAM implements practices for assocation mapping, based on those described in Servin, B and Stephens,Office Home And Business 2010 Key, M (2007). Imputation-based evaluation of association scientific tests: candidate genes and quantitative traits. PLoS Genetics, 2007. BIMBAM can handle both large association reports (e.g., genome scans) and scaled-down 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: computer software for haplotype reconstruction,Office 2007 License, and estimating missing genotypes from population information The program fastPHASE implements strategies described in Scheet, P and Stephens, M (2006). A fast and flexible statistical product 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 computer software is free for non-commercial use, and may possibly be licensed for commercial use. To view the terms and conditions, and then proceed to download, click here. PHASE: software system for haplotype reconstruction, and recombination rate estimation from population info The program PHASE implements tactics for estimating haplotypes from population genotype data described in Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian approaches for haplotype reconstruction from population genotype data. American Journal of Human Genetics,Purchase Windows 7, 73:1162-1169. Stephens, M., Smith, N., and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population information. American Journal of Human Genetics, 68, 978--989. Stephens,Office Professional Plus 2010, 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 application 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 program is free for non-commercial use, and may very well 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, 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, so allele frequencies are estimated at any presented location by using observed genotypes at near-by sampling locations, with data at the nearest sampling locations being provided greatest weight. Details are provided 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 towards the ivory trade. Proc Natl Acad Sci U S A, 41:14844-14852, 2004. SCAT is available here. HOTSPOTTER: software system for identifying recombination hotspots from population SNP information This software package by Na Li implements practices from:
N Li and M Stephens. Modeling linkage disequilibrium and identifying recombination hotspots utilising single-nucleotide polymorphism info. 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