hidden markov model matlab source code dna

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.smashr: R package for adaptive Gaussian and Poisson.SCAT: Smoothed and Continuous AssignmenTs.RSS: Regression with Summary Statistics.Studies, via Bayesian Variable Selection Regression piMASS: Multi-SNP analysis for Genetic Association.Recombination rate estimation from population data PHASE: software for haplotype reconstruction, and.mvBIMBAM: software for genetic association analysis.msCentipede: inference of transcription factorīinding from chromatin accessibility data.MethylHMM: inference under hidden Markov models.Testing of multiple effects on multiple outcomes/conditions

mashr: R package for Empirical Bayes estimation and.Recombination hotspots from population SNP data Population structure from SNP genotype data fastStructure: variational inference of.fastPHASE: software for haplotype reconstruction,Īnd estimating missing genotypes from population data.eQtlBma: software to detect eQTLs by Bayesian Model.EEMS: Estimated Effective Migration Surfaces.

RNA-Seq expression data using Grade of Membership models

CountClust: R package for clustering and visualizing.

BRIdGE: Bayesian Regression for Identifying.

BLIMP: software for Best Linear IMPutation.

BIMBAM: software for Bayesian IMputation-Based.

Github Page for new software in development from the Stephens

Hidden markov model matlab source code dna