A statistical perspective on the challenges in molecular microbial biology

DOI10.1007/S13253-021-00447-1OpenAlexW3136341404MaRDI QIDQ2084409FDOQ2084409

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

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

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

Uses Software

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

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