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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Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women
Despina Tsementzi,Angela Pena-Gonzalez,Jinbing Bai,Yi-Juan Hu,Pretesh Patel,Joseph W. Shelton,Mary Dolan,Jessica Arluck,Namita Khanna,Lesley B. Conrad,Isabelle Scott,Tony Y. Eng,Konstantinos T. Konstantinidis,Deborah Watkins Bruner +13 more
TL;DR: While the importance of commensal microbes in vaginal health is well appreciated, little is known about the effects of gynecological cancer and radiation therapy on the vaginal microbiome of postmenopausal women.
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MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities
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Archaeal biogeography and interactions with microbial community across complex subtropical coastal waters
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An active bacterial community linked to high chl-a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community
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References
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TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
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QIIME allows analysis of high-throughput community sequencing data.
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Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
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Metagenomic biomarker discovery and explanation
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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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