Differential abundance analysis for microbial marker-gene surveys
TLDR
It is shown that metagenomeSeq outperforms the tools currently used in this field and relies on a novel normalization technique and a statistical model that accounts for undersampling in large-scale marker-gene studies.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.read more
Citations
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Journal ArticleDOI
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.
TL;DR: The primary workflows and software used for both approaches are reviewed, including whole-genome shotgun sequencing and marker gene, and the current challenges in the field are discussed.
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Analysis and correction of compositional bias in sparse sequencing count data
M. Senthil Kumar,Eric V. Slud,Eric V. Slud,Kwame Okrah,Stephanie C. Hicks,Sridhar Hannenhalli,Héctor Corrada Bravo +6 more
TL;DR: It is argued that detailed experiments specifically addressing the influence of compositional bias in metagenomics are needed, and an empirical Bayes normalization approach is proposed to overcome this problem.
Journal ArticleDOI
Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System.
TL;DR: In this study, bacteriomes of eight karst caves in southwest China were examined, and co-occurrence networks of cave bacterial communities were constructed, which suggest that the distribution of bacterial communities is driven more by sample types than the separate caves from which samples were collected.
Journal ArticleDOI
Epiviz: interactive visual analytics for functional genomics data
TL;DR: Epiviz (http://epiviz.umd.edu/), a web-based genome browser, and the Epivizr Bioconductor package allow interactive, extensible and reproducible visualization within a state-of-the-art data-analysis platform.
Journal ArticleDOI
Fecal and blood microbiota profiles and presence of nonalcoholic fatty liver disease in obese versus lean subjects.
Yeojun Yun,Han Na Kim,Eun-Ju Lee,Seungho Ryu,Yoosoo Chang,Hocheol Shin,Hyung Lae Kim,Tae-Hun Kim,Kwon Yoo,Hwi Young Kim +9 more
TL;DR: Fecal and blood microbiota profiles showed different patterns between subjects with obese and lean NAFLD, which might be potential biomarkers to discriminate diverse phenotypes ofNAFLD.
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TL;DR: A new method for metagenomic biomarker discovery is described and validates by way of class comparison, tests of biological consistency and effect size estimation to address the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.
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