A statistical perspective on the challenges in molecular microbial biology

DOI10.1007/S13253-021-00447-1MaRDI QIDQ2084409zbMATH OpenOpenAlexFDO

Authors P. Jeganathan, Susan Holmes

Publication date 18 October 2022

Published in Journal of Agricultural, Biological and Environmental Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2103.04198

zbMATH Keywords

microbial ecologyquality controllatent Dirichlet allocationBayesian data analysisBayesian nonparametric ordinationhierarchical mixture modelssequencing data

Mathematics Subject Classification ID

Applications of statistics to environmental and related topics (62P12)

Cites work

• A nonparametric spatial test to identify factors that shape a microbiome
• Adaptive gPCA: a method for structured dimensionality reduction with applications to microbiome data
• Analysis of a data matrix and a graph: metagenomic data and the phylogenetic tree
• Bioinformatics and computational biology solutions using R and Bioconductor.
• Doing Bayesian data analysis. A tutorial introduction with R, JAGS, and Stan
• Estimation and prediction for stochastic blockmodels for graphs with latent block structure
• From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis
• Generalized discriminant analysis based on distances
• Inference from iterative simulation using multiple sequences
• Interactive Visualization of Hierarchically Structured Data
• MIMIX: a Bayesian mixed-effects model for microbiome data from designed experiments
• Multivariate data analysis: The French way
• THE TRANSFORMATION OF POISSON, BINOMIAL AND NEGATIVE-BINOMIAL DATA
• The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples
• ggplot2. Elegant graphics for data analysis. With contributions by Carson Sievert

Cited in

(3)

• Power transformations of relative count data as a shrinkage problem
• Microbiome Subcommunity Learning with Logistic-Tree Normal Latent Dirichlet Allocation
• Bayesian variable selection for high-dimensional rank data

Describes a project that uses

Uses Software

• DADA2
• MIMIX
• DESMAN
• structSSI
• adaptiveGPCA
• NBC
• Voom
• Phyloseq
• limma
• DEseq
• Stan
• JAGS
• ggplot2
• edgeR
• gcrma
• vegan
• Bioconductor
• R

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