ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes Export

@article{citeulike:5632094, abstract = {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. 10.1093/bioinformatics/btp508}, author = {Kristiansson, Erik and Hugenholtz, Philip and Dalevi, Daniel}, citeulike-article-id = {5632094}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp508}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/20/2737.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/20/2737.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/20/2737#B13}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19696045}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19696045}, day = {15}, doi = {10.1093/bioinformatics/btp508}, journal = {Bioinformatics}, keywords = {comparative, metagenomics, r, statistics}, month = {October}, number = {20}, pages = {2737--2738}, posted-at = {2009-11-03 15:14:37}, priority = {2}, title = {ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes}, url = {http://dx.doi.org/10.1093/bioinformatics/btp508}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:5632094 L3 - citeulike-article-id:5632094 N2 - 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. 10.1093/bioinformatics/btp508 IS - 20 JF - Bioinformatics EP - 2738 TI - ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes VL - 25 SP - 2737 KW - comparative KW - metagenomics KW - r KW - statistics AU - Kristiansson, Erik AU - Hugenholtz, Philip AU - Dalevi, Daniel PY - 2009/10/15/ UR - http://dx.doi.org/10.1093/bioinformatics/btp508 ER -