ExperimentHub

ExperimentHub provides access to curated metagenomic datasets and standardized per-participant metadata from sources including the Human Microbiome Project to support comparative taxonomic and functional microbiome analyses.

Key Features:

• Centralized data aggregation: Aggregates thousands of metagenomic profiles with bacterial, fungal, archaeal, and viral taxonomic abundances and quantitative metabolic functional profiles from public sources including the Human Microbiome Project.
• Standardized per-participant metadata: Associates comprehensive participant-level metadata with datasets to support stratified and covariate-aware analyses.
• Cloud-based distribution and Bioconductor/R integration: Distributes data via cloud-based resources with programmatic access and integration into the Bioconductor/R ecosystem.
• Local caching for reproducibility: Maintains a local cache of retrieved files to enable reproducible and efficient reuse of datasets.
• Open source pipelines: Builds and expands the resource using open source software and pipelines to facilitate integration of new microbiome datasets.

Scientific Applications:

• Taxonomic and functional correlation analysis: Explore relationships between microbial taxa and quantitative metabolic functional profiles.
• Gut enterotype investigation: Investigate distinct gut microbial community structures (enterotypes) across cohorts.
• Comparative disease classification: Compare disease classification accuracy across different types of metagenomic data.

Methodology:

Data are distributed via cloud-based resources, provided with standardized metadata including taxonomic abundances and quantitative metabolic functional profiles, cached locally for reproducible access, and implemented using open source software and pipelines with integration into Bioconductor/R.