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
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.