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ampvis2: an R package to analyse and visualise 16S rRNA amplicon data

View ORCID ProfileKasper S. Andersen, View ORCID ProfileRasmus H. Kirkegaard, View ORCID ProfileSøren M. Karst, Mads Albertsen
doi: https://doi.org/10.1101/299537
Kasper S. Andersen
1Center for Microbial Communities, Aalborg University, Frederik Bajers vej 7H, 9220 Aalborg East, Denmark
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Rasmus H. Kirkegaard
1Center for Microbial Communities, Aalborg University, Frederik Bajers vej 7H, 9220 Aalborg East, Denmark
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Søren M. Karst
1Center for Microbial Communities, Aalborg University, Frederik Bajers vej 7H, 9220 Aalborg East, Denmark
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Mads Albertsen
1Center for Microbial Communities, Aalborg University, Frederik Bajers vej 7H, 9220 Aalborg East, Denmark
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Abstract

Summary Microbial community analysis using 16S rRNA gene amplicon sequencing is the backbone of many microbial ecology studies. Several approaches and pipelines exist for processing the raw data generated through DNA sequencing and convert the data into OTU-tables. Here we present ampvis2, an R package designed for analysis of microbial community data in OTU-table format with focus on simplicity, reproducibility, and sample metadata integration, with a minimal set of intuitive commands. Unique features include flexible heatmaps and simplified ordination. By generating plots using the ggplot2 package, ampvis2 produces publication-ready figures that can be easily customised. Furthermore, ampvis2 includes features for interactive visualisation, which can be convenient for larger, more complex data.

Availability ampvis2 is implemented in the R statistical language and is released under the GNU A-GPL license. Documentation website and source code is maintained at: https://github.com/MadsAlbertsen/ampvis2

Contact Mads Albertsen (ma{at}bio.aau.dk)

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 11, 2018.
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ampvis2: an R package to analyse and visualise 16S rRNA amplicon data
Kasper S. Andersen, Rasmus H. Kirkegaard, Søren M. Karst, Mads Albertsen
bioRxiv 299537; doi: https://doi.org/10.1101/299537
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ampvis2: an R package to analyse and visualise 16S rRNA amplicon data
Kasper S. Andersen, Rasmus H. Kirkegaard, Søren M. Karst, Mads Albertsen
bioRxiv 299537; doi: https://doi.org/10.1101/299537

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