ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

Kristiansson, Erik,1978Gothenburg University,Göteborgs universitet,Zoologiska institutionen, zoofysiologi,Institutionen för neurovetenskap och fysiologi, sektionen för fysiologi,Department of Zoology, Zoophysiology,Institute of Neuroscience and Physiology, Department of Physiology,University of Gothenburg (author)

Summary: Microorganisms are ubiquitous in nature and constitute intrinsic parts of almost every ecosystem. A culture-independent and powerful way to study microbial communities is metagenomics. In such studies, functional analysis is performed on fragmented genetic material from multiple species in the community. The recent advances in high-throughput sequencing have greatly increased the amount of data in metagenomic projects. At present, there is an urgent need for efficient statistical tools to analyse these data. We have created ShotgunFunctionalizeR, an R-package for functional comparison of metagenomes. The package contains tools for importing, annotating and visualizing metagenomic data produced by shotgun high-throughput sequencing. ShotgunFunctionalizeR contains several statistical procedures for assessing functional differences between samples, both for individual genes and for entire pathways. In addition to standard and previously published methods, we have developed and implemented a novel approach based on a Poisson model. This procedure is highly flexible and thus applicable to a wide range of different experimental designs. We demonstrate the potential of ShotgunFunctionalizeR by performing a regression analysis on metagenomes sampled at multiple depths in the Pacific Ocean.

Hugenholtz, Philip (author)
Dalevi, Daniel,1974Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)dalevi (author)
Göteborgs universitetZoologiska institutionen, zoofysiologi (creator_code:org_t)

By the author/editor: Kristiansson, Er ...; Hugenholtz, Phil ...; Dalevi, Daniel, ...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

NATURAL SCIENCES: NATURAL SCIENCES; and Mathematics; and Probability Theo ...

By the university: University of Gothenburg; Chalmers University of Technology

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