curatedMetagenomicData is a Bioconductor package providing uniformly processed and manually annotated human microbiome profiles for thousands of people already included and planned for inclusion in the database. Microbial taxonomy and metabolic functional potential can be analyzed with respect to numerous participant characteristics and health outcomes, simply and reproducibly on a normal laptop.
Each dataset provides taxonomic abundance, gene marker presence and absence (from MetaPhlAn2), plus coverage and abundance of metabolic pathways and gene families abundance (from HUMAnN2). Metagenomic data with matched health and socio-demographic data are provided as Bioconductor ExpressionSet objects, with options for automatic conversion of taxonomic profiles to phyloseq or metagenomeSeq objects for microbiome-specific analyses. For more detail, see the pre-print and the Analyses menu item above.
curatedMetagenomicData aims to embody the spirit of open-source software, reproducibility, and to provide an ever growing collection of metagenomic data provided under the Artistic License 2.0. Please visit the CONTRIBUTING page if you are willing to contribute reports of bugs and curation errors, suggest relevant new datasets, or provide curation and code.