Differential abundance analysis for microbial marker-gene surveys

Joseph N. Paulson; O. Colin Stine; Héctor Corrada Bravo; Mihai Pop

doi:10.1038/nmeth.2658

Differential abundance analysis for microbial marker-gene surveys

Joseph N. Paulson, O. Colin Stine, Héctor Corrada Bravo, Mihai Pop

Research output: Contribution to journal › Article › peer-review

850 Scopus citations

Abstract

We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling - a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field.

Original language	English (US)
Pages (from-to)	1200-1202
Number of pages	3
Journal	Nature Methods
Volume	10
Issue number	12
DOIs	https://doi.org/10.1038/nmeth.2658
State	Published - Dec 2013
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Molecular Biology
Biochemistry
Cell Biology

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10.1038/nmeth.2658

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year = "2013",

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Differential abundance analysis for microbial marker-gene surveys

Abstract

ASJC Scopus subject areas

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