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![]() Best Denoise 2017 Software In Developmentsmashr: R package for adaptive GaussianSmashr is an R package implementing "adaptive shrinkage" methodsFor signal denoising applications, including smoothing of Poisson andHeteroskedastic Gaussian data. See the following paper for details of the model andFor estimating and testing effects in genomic studies with multiple WaveQTL: a wavelet-based approach for geneticAssociation analysis of functional phenotypesEstimation and testing of multiple effects on multipleThe mashr package implements methods to estimate and test manyEffects in many conditions (or many effects on many outcomes).The methods use Empirical Bayes methods to estimate patterns ofSimilarity among conditions, and then exploit those patterns ofSimilarity among conditions to improve accuracy of effectEstimates. Variational inference for Bayesian variable smashr: R package for adaptive Gaussian and Poisson SCAT: Smoothed and Continuous AssignmenTs Biostatistics 18(2): 275-294. ashr: R package for adaptive shrinkage.The ashr ("Adaptive SHrinkage in R") package aims to provide simple,Generic, and flexible methods to derive "shrinkage-based" estimatesAnd credible intervals for unknown quantities, given only estimates ofThose quantities and their corresponding estimated standard errors.The software is based on methods described in the followingRates: a new deal. RSS is basedOn the statistical framework introduced in the following paper:Multiple regression with summary statistics from genome-wideTo appear in Annals of Applied Statistics.MATLAB code implementing the methods is available on RSS: Regression with Summary Statistics.The RSS software implements Bayesian large-scale multipleRegression methods that can be applied to summary data. Smoothing via Adaptive Shrinkage (smash):Denoising Poisson and heteroskedastic Gaussian signals. Visual basic for applications install macNature Genetics 48: 94-100.The software and C++ source code can be downloaded from The software is based on theD Petkova, J Novembre, and M Stephens (2016).Population structure with estimated effective migration surfaces. EEMS uses the conceptOf effective migration to model the relationship between genetics andGeography, and it outputs an "estimated effective migration surface" That is, a visual representation of population structure that canHighlight potential regions of higher-than-average andLower-than-average historic gene flow. PLoS GeneticsEEMS is software for analyzing and visualizing spatial populationStructure from geo-referenced genetic samples. The R package is based on the methods described in:Expression data using grade of membership models. ![]() Sequence data arisingFrom high-throughput sequencing assays), as described in:Wavelet-based genetic association analysis of functional phenotypesArising from high-throughput sequencing assays. PLoS ONE 8(7): e65245.Information and to download the software.WaveQTL is a software implementing a wavelet-based approach forGenetic association analysis of functional phenotypes (e.g. A Unified framework for association analysis withMultiple related phenotypes. PLoS ONEM Stephens (2013). mvBIMBAM: software for genetic associationMvBIMBAM, a version of BIMBAM for multivariate association analysis,Implements a Bayesian approach for genetic associationAnalysis of multiple related phenotypes, as described in:A multivariate genome-wide association analysisOf 10 LDL subfractions, and their response to statin treatment, in 1868 Caucasians. ![]() For details, see theLICENSE.txt file included with this software package.Variational inference for Bayesian variable selectionThis is a MATLAB implementation of the variational inference methodFor Bayesian variable selection described in a forthcoming BayesianGet more information, and to download the software.
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