Journal Article

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

Erik Kristiansson, Philip Hugenholtz and Daniel Dalevi

in Bioinformatics

Volume 25, issue 20, pages 2737-2738
Published in print October 2009 | ISSN: 1367-4803
Published online August 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp508
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

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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.

Availability: http://shotgun.zool.gu.se

Contact: dalevi@chalmers.se; erik.kristiansson@zool.gu.se

Supplementary information: supplementary data are available at Bioinformatics online.

Journal Article.  1191 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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