Highlight potential regions of higher-than-average and That is, a visual representation of population structure that can Geography, and it outputs an "estimated effective migration surface" Of effective migration to model the relationship between genetics and Structure from geo-referenced genetic samples. PLoS GeneticsĮEMS is software for analyzing and visualizing spatial population The R package is based on the methods described in:Įxpression data using grade of membership models. Memberships, and generating a visual summary of the cluster Models (also admixture models) to cluster RNA-seq gene expressionĬount data, identifying characteristic genes driving cluster Visualizing RNA-Seq expression data using Grade of Membership models.ĬountClust provides functions for fitting grade-of-membership CountClust: R package for clustering and.The software is based on methods described in the following Those quantities and their corresponding estimated standard errors. Generic, and flexible methods to derive "shrinkage-based" estimatesĪnd credible intervals for unknown quantities, given only estimates of The ashr ("Adaptive SHrinkage in R") package aims to provide simple, ashr: R package for adaptive shrinkage.
#HOTSPOTTER SOFTWARE FOR MAC CODE#
MATLAB code implementing the methods is available on To appear in Annals of Applied Statistics. Multiple regression with summary statistics from genome-wide On the statistical framework introduced in the following paper: Regression methods that can be applied to summary data. The RSS software implements Bayesian large-scale multiple RSS: Regression with Summary Statistics.Smoothing via Adaptive Shrinkage (smash):ĭenoising Poisson and heteroskedastic Gaussian signals. Smashr is an R package implementing "adaptive shrinkage" methodsįor signal denoising applications, including smoothing of Poisson and smashr: R package for adaptive Gaussian.See the following paper for details of the model andįor estimating and testing effects in genomic studies with multiple Similarity among conditions to improve accuracy of effectĮstimates. Similarity among conditions, and then exploit those patterns of The methods use Empirical Bayes methods to estimate patterns of The mashr package implements methods to estimate and test manyĮffects in many conditions (or many effects on many outcomes). WaveQTL: a wavelet-based approach for geneticĪssociation analysis of functional phenotypesĮstimation and testing of multiple effects on multiple.Variational inference for Bayesian variable.
Testing of multiple effects on multiple outcomes/conditions
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