Improved variational Bayes inference for transcript expression estimation

DOI10.1515/SAGMB-2013-0054MaRDI QIDQ743618zbMATH OpenOpenAlexWikidataFDO

Authors Panagiotis Papastamoulis, James Hensman, Peter Glaus, Magnus Rattray

Publication date 25 September 2014

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Copyright license Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International

Full work available at URL https://doi.org/10.1515/sagmb-2013-0054

zbMATH Keywords

mixture modelKullback-Leibler divergencegeneralized Dirichlet distributionBitSeqmarginal likelihood bound

Mathematics Subject Classification ID

Bayesian inference (62F15) General biostatistics (92B15) Protein sequences, DNA sequences (92D20)

Recommendations

• Bayesian Inference for Gene Expression and Proteomics
• A Bayesian Framework for Statistical Inference from Gene Expression Data
• Bayesian Modeling of Differential Gene Expression
• Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes
• Bayesian estimation of differential transcript usage from RNA-seq data
• A semi-parametric Bayesian approach for differential expression analysis of RNA-seq data
• Bayesian inference for gene expression and proteomics.
• A Bayesian Model for Cross-Study Differential Gene Expression
• A Bayesian Mixture Model for Differential Gene Expression

Cites work

• scientific article; zbMATH DE number 3567782 (Why is no real title available?)
• Adaptive stochastic approximation by the simultaneous perturbation method
• An introduction to variational methods for graphical models
• Estimating marginal likelihoods for mixture and Markov switching models using bridge sampling techniques*
• Finite mixture and Markov switching models.
• Finite mixture models
• Generalized Dirichlet distribution in Bayesian analysis
• Marginal Likelihood from the Gibbs Output
• Markov chain Monte Carlo methods and the label switching problem in Bayesian mixture modeling
• Multivariate stochastic approximation using a simultaneous perturbation gradient approximation
• Parameter estimation for generalized Dirichlet distributions from the sample estimates of the first and the second moments of random variables
• Sampling-Based Approaches to Calculating Marginal Densities
• The Calculation of Posterior Distributions by Data Augmentation
• Variational approximations in Bayesian model selection for finite mixture distributions

Cited in

(5)

• Variational Bayesian approach for analyzing interval-censored data under the proportional hazards model
• Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth.
• Exact transcript quantification over splice graphs
• Bayesian estimation of differential transcript usage from RNA-seq data
• Deconvolution of base pair level RNA-seq read counts for quantification of transcript expression levels

Describes a project that uses

Uses Software

• TopHat

This page was built for publication: Improved variational Bayes inference for transcript expression estimation

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q743618)