Microbiome Datasets Are Compositional: And This Is Not Optional
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Summary
The purpose of this review is to alert investigators to the dangers inherent in ignoring the compositional nature of the data, and point out that HTS datasets derived from microbiome studies can and should be treated as compositions at all stages of analysis.
- Type
- review
- Published
- 2017-11-15
- Cited by
- 2,566
- References
- 46
- Access
- Open access
- OpenAlex
- https://openalex.org/W2769542288
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:23138321
Keywords
Microbiome, Computer science, Compositional data, Metagenomics, Computational biology
References
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- Mathematical contributions to the theory of evolution.—On a form of spurious correlation which may arise when indices are used in the measurement of organs
- ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq
- Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
- Principal component analysis of compositional data
- UniFrac: an effective distance metric for microbial community comparison
- phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
- Control of catalytic efficiency by a coevolving network of catalytic and noncatalytic residues
- zCompositions — R package for multivariate imputation of left-censored data under a compositional approach
- Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis
- A scaling normalization method for differential expression analysis of RNA-seq data
- Biplots of Compositional Data
- Proportionality: A Valid Alternative to Correlation for Relative Data
- Inferring Correlation Networks from Genomic Survey Data
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- Toward an improved definition of a healthy microbiome for healthy aging
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- Uncovering the drivers of animal-host microbiotas with joint distribution modeling
- q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data
- Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth
- Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis
- Linear association in compositional data analysis
- Genome watch: Keeping tally in the microbiome
- Characterization of Urinary Microbiome and Their Association with Health and Disease
- Long-term seasonality of marine photoheterotrophic bacteria reveals low cohesiveness within the different phylogroups
- Uncovering the drivers of host-associated microbiota with joint species distribution modelling
- Data on the gut and saliva microbiota from a cohort of atherosclerosis patients determined by 16S rRNA gene sequencing
- Ureide metabolism in plant-associated bacteria: purine plant-bacteria interactive scenarios under nitrogen deficiency
- Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils
- Akkermansia muciniphila as a Model Case for the Development of an Improved Quantitative RPA Microbiome Assay
- Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
- Influent salinity conditions affect the bacterial communities of biofouling in hybrid MBBR-MBR systems
- From hairballs to hypotheses–biological insights from microbial networks
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