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phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
R

README.md

phyloseq

Article on Improved Microbiome Analysis

McMurdie and Holmes (2014) Waste Not, Want Not: Why Rarefying Microbiome Data is Statistically Inadmissible PLoS Computational Biology 10(4): e1003531

Presubmission versions ahead of acceptance (2013): PDF version 2, PDF version 1

Latest peer-reviewed article about phyloseq

phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data (2013) PLoS ONE 8(4):e61217

Interface with microbio.me/qiime

See the microbio_me_qiime tutorial for more details and examples downloading and importing into phyloseq/R directly from this public database.

Other resources

The phyloseq project also has a number of supporting online resources, most of which can by found at the phyloseq home page, or from the phyloseq stable release page on Bioconductor.

To post feature requests or ask for help, try the phyloseq Issue Tracker.

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