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ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
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- Kristiansson, Erik, 1978 (author)
- Gothenburg 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
- Hugenholtz, Philip (author)
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- Dalevi, Daniel, 1974 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
- (creator_code:org_t)
- 2009
- 2009
- English.
- In: Bioinformatics. - 1367-4803 .- 1367-4811. ; 25:20, s. 2737-2738
- Journal article (peer-reviewed)
Abstract
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- NATURVETENSKAP -- Matematik -- Sannolikhetsteori och statistik (hsv//swe)
- NATURAL SCIENCES -- Mathematics -- Probability Theory and Statistics (hsv//eng)
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