Program to evaluate microbial communities using sequence data

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dc.contributor.author Garrett, Karen A.
dc.contributor.author Gomez-Montano, Lorena
dc.contributor.author Jumpponen, Ari M.
dc.date.accessioned 2013-08-07T21:35:53Z
dc.date.available 2013-08-07T21:35:53Z
dc.date.issued 2013-10-01
dc.identifier.uri http://hdl.handle.net/2097/16206
dc.description Citation: Gomez-Montano, L. Jumpponen, A., Gonzales, M., . . . Garrett, K. (2013). Do bacterial and fungal communities in soils of the Bolivian Altiplano change under shorter fallow periods?. Soil Biology & Biochemistry, 65, 50-59. https://doi.org/10.1016/j.soilbio.2013.04.005
dc.description.abstract This R script performs statistical analyses using sequence data. It goes through all the steps from reading the data into R, merging multiple datasets, calculating diversity metrics, performing statistical analysis such as linear regression and non-metric multidimensional scaling (NMDS), making graphs and saving and exporting them for use in presentations and publications. It illustrates the analyses used in Gomez-Montano et al. 2013, and can be used as a template for other similar analyses. Sections: 1. Preparing data 2. Diversity metrics 3. Analysis of individual OTU frequencies 4. Soil physical and chemical analyses 5. NMDS community analysis en_US
dc.language.iso en_US en_US
dc.relation.uri https://doi.org/10.1016/j.soilbio.2013.04.005
dc.rights This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).
dc.rights.uri https://www.elsevier.com/about/policies/sharing
dc.rights.uri https://rightsstatements.org/vocab/InC/1.0/
dc.subject Bacterial communities en_US
dc.subject Fungal communities en_US
dc.subject High-throughput sequencing en_US
dc.subject Metagenomics en_US
dc.subject R programming environment en_US
dc.subject Non-metric multidimensional scaling en_US
dc.title Program to evaluate microbial communities using sequence data en_US
dc.type Article en_US
dc.date.published 2013 en_US
dc.citation.doi 10.1016/j.soilbio.2013.04.005
dc.citation.epage 59
dc.citation.issn 0038-0717
dc.citation.issue 65
dc.citation.jtitle Soil Biology & Biochemistry
dc.citation.spage 50
dc.citation Gomez-Montano, L. Jumpponen, A., Gonzales, M., . . . Garrett, K. (2013). Do bacterial and fungal communities in soils of the Bolivian Altiplano change under shorter fallow periods?. Soil Biology & Biochemistry, 65, 50-59. https://doi.org/10.1016/j.soilbio.2013.04.005
dc.contributor.authoreid kgarrett en_US
dc.contributor.authoreid ari en_US
dc.description.version Article: Author's Manuscript


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