Cargando…

Robust Differential Abundance Analysis of Microbiome Sequencing Data

It is well known that the microbiome data are ridden with outliers and have heavy distribution tails, but the impact of outliers and heavy-tailedness has yet to be examined systematically. This paper investigates the impact of outliers and heavy-tailedness on differential abundance analysis (DAA) us...

Descripción completa

Detalles Bibliográficos
Autores principales:	Li, Guanxun, Yang, Lu, Chen, Jun, Zhang, Xianyang
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2023
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10671797/ https://www.ncbi.nlm.nih.gov/pubmed/38002943 http://dx.doi.org/10.3390/genes14112000

Ejemplares similares

LinDA: linear models for differential abundance analysis of microbiome compositional data
por: Zhou, Huijuan, et al.
Publicado: (2022)

Pairwise ratio-based differential abundance analysis of infant microbiome 16S sequencing data
por: Mildau, Kevin, et al.
Publicado: (2023)

microbiomeDASim: Simulating longitudinal differential abundance for microbiome data
por: Williams, Justin, et al.
Publicado: (2020)

benchdamic: benchmarking of differential abundance methods for microbiome data
por: Calgaro, Matteo, et al.
Publicado: (2022)

Robust methods for differential abundance analysis in marker gene surveys
por: Paulson, Joseph N., et al.
Publicado: (2013)

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data
por: Chen, Li, et al.
Publicado: (2018)

An empirical Bayes approach to normalization and differential abundance testing for microbiome data
por: Liu, Tiantian, et al.
Publicado: (2020)

Investigating differential abundance methods in microbiome data: A benchmark study
por: Cappellato, Marco, et al.
Publicado: (2022)

Predictive Modeling of Microbiome Data Using a Phylogeny-Regularized Generalized Linear Mixed Model
por: Xiao, Jian, et al.
Publicado: (2018)

An Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis
por: Banerjee, Kalins, et al.
Publicado: (2019)

Relative abundance data can misrepresent heritability of the microbiome
por: Bruijning, Marjolein, et al.
Publicado: (2023)

A maximum-type microbial differential abundance test with application to high-dimensional microbiome data analyses
por: Li, Zhengbang, et al.
Publicado: (2022)

BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations
por: Rahman, Gibraan, et al.
Publicado: (2023)

Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values
por: Ahn, Seungjun, et al.
Publicado: (2023)

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data
por: Wadsworth, W. Duncan, et al.
Publicado: (2017)

Identification of low abundance microbiome in clinical samples using whole genome sequencing
por: Zhang, Chao, et al.
Publicado: (2015)

Microbiome differential abundance methods produce different results across 38 datasets
por: Nearing, Jacob T., et al.
Publicado: (2022)

mbImpute: an accurate and robust imputation method for microbiome data
por: Jiang, Ruochen, et al.
Publicado: (2021)

Testing for differential abundance in mass cytometry data
por: Lun, Aaron T. L., et al.
Publicado: (2017)

A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions
por: Yang, Lu, et al.
Publicado: (2022)

Multiscale adaptive differential abundance analysis in microbial compositional data
por: Wang, Shulei
Publicado: (2023)

Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies
por: Kodalci, Leyla, et al.
Publicado: (2023)

Erratum to: An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data
por: Wadsworth, W. Duncan, et al.
Publicado: (2017)

LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control
por: Hu, Yingtian, et al.
Publicado: (2022)

SDA: a semi-parametric differential abundance analysis method for metabolomics and proteomics data
por: Li, Yuntong, et al.
Publicado: (2019)

The accuracy of absolute differential abundance analysis from relative count data
por: Roche, Kimberly E., et al.
Publicado: (2022)

Robustly detecting differential expression in RNA sequencing data using observation weights
por: Zhou, Xiaobei, et al.
Publicado: (2014)

RFtest: A Robust and Flexible Community-Level Test for Microbiome Data Powerfully Detects Phylogenetically Clustered Signals
por: Zhang, Lujun, et al.
Publicado: (2022)

Abundance alteration of nondominant species in fecal-associated microbiome of patients with SAPHO syndrome
por: Zhen, Jianhua, et al.
Publicado: (2021)

High Oscillospira abundance indicates constipation and low BMI in the Guangdong Gut Microbiome Project
por: Chen, Yi-ran, et al.
Publicado: (2020)

Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano
por: Banskar, Sunil, et al.
Publicado: (2016)

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data
por: Thang, Mike W.C., et al.
Publicado: (2019)

Author Correction: Microbiome differential abundance methods produce different results across 38 datasets
por: Nearing, Jacob T., et al.
Publicado: (2022)

High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome
por: Wen, Tao, et al.
Publicado: (2020)

Altered vaginal microbiome and relative co-abundance network in pregnant women with penicillin allergy
por: Li, Xiaohua, et al.
Publicado: (2020)

Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing
por: Wallen, Zachary D.
Publicado: (2021)

MGnify: the microbiome sequence data analysis resource in 2023
por: Richardson, Lorna, et al.
Publicado: (2022)

Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues
por: Kartti, Souad, et al.
Publicado: (2023)

Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations
por: Scire, Jérémie, et al.
Publicado: (2022)

Controlling taxa abundance improves metatranscriptomics differential analysis
por: Ji, Zhicheng, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_urkah634cqd5u0mpb1bfdfb7uq