What curatedMetagenomicData provides | Additional documentation and resources | Installation | R Packages | Sample Metadata | Data Access | curatedMetagenomicData() | mergeData() | returnSamples() | Example Analysis | Load R packages | Retrieve harmonized metadata | Prepare Data | Return Samples | Agglomerate By Taxonomic Rank | Alpha Diversity | Beta Diversity | Bray–Curtis PCoA | UMAP | Differential Abundance | Type Conversion | Session Info

The Pipeline | Installation | Load Package | Finding Data | Getting Data | No Metadata? | ML Analysis? | Session Info

Installation | Introduction | Example Data | Construction | Manipulation | Session Info

Publications | Prerequisites | Introduction | Features | Frequency Table Generation | Straightforward Subsetting | HMP Controlled-Access Participant Data | Apply for dbGaP Access | Install the SRA Toolkit | Merge with HMP16SData | Analysis Using the phyloseq Package | Coercion to phyloseq Objects | Alpha Diversity Analysis | Beta Diversity Analysis | Principle Coordinates Analysis | Phylum-level Comparison to Metagenomic Shotgun Sequencing | Exporting Data to CSV, SAS, SPSS, and STATA Formats | Prepare Data for Export | Export to CSV Format | Export to SAS Format | Export to SPSS Format | Export to STATA Format | Session Information

Publications | Prerequisites | Introduction | Features | Frequency Table Generation | Straightforward Subsetting | HMP Controlled-Access Participant Data | Apply for dbGaP Access | Install the SRA Toolkit | Merge with HMP16SData | Analysis Using the phyloseq Package | Coercion to phyloseq Objects | Alpha Diversity Analysis | Beta Diversity Analysis | Principle Coordinates Analysis | Phylum-level Comparison to Metagenomic Shotgun Sequencing | Exporting Data to CSV, SAS, SPSS, and STATA Formats | Prepare Data for Export | Export to CSV Format | Export to SAS Format | Export to SPSS Format | Export to STATA Format | Session Information