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