phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
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Cites methods from "phyloseq: an R package for reproduc..."
...org/ [2014]), utilizing the phyloseq package (McMurdie and Holmes, 2013) to import sample data and calculate alphaand beta-diversity metrics....
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References
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"phyloseq: an R package for reproduc..." refers background or methods in this paper
...clustering output formats like QIIME [11], mothur [12], the RDP-...
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...packages/pipelines, including QIIME [11], mothur [12], and...
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...We would also like to thank the developers of the open source packages on which phyloseq depends, in particular Rob Knight and his lab for QIIME [11], Hadley Wickham for the ggplot2 [57], reshape [89], and plyr [90] packages, as well as the Bioconductor and R teams [24,34]....
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...Virtual machine image and cloud-deployed ‘‘pipeline’’ analyses [11,15,19] can further increase accessibility of analyses...
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...Instead, phyloseq provides tools to read the output files of the most common OTU-clustering applications [7,11,12,14], and represents this data in R as an instance of the main data class....
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17,350 citations
"phyloseq: an R package for reproduc..." refers methods in this paper
...Instead, phyloseq provides tools to read the output files of the most common OTU-clustering applications [7,11,12,14], and represents this data in R as an instance of the main data class....
[...]
...clustering output formats like QIIME [11], mothur [12], the RDP-...
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...packages/pipelines, including QIIME [11], mothur [12], and...
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...This PDF file contains a table summarizing a comparison of supported capabilities between phyloseq and QIIME [11], mothur [12], and the pair of packages OTUbase [35] and mcaGUI [88]....
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