| Class | Description |
|---|---|
| AddMetadataToPathwayTables |
This BioModule is used to add metadata columns to the HumanN2 pathway abundance, pathway coverage, and gene family
tables.
|
| Humann2CountModule |
This abstract superclass is extended by all other modules in this package.
Shared method implementations are defined to ensure uniform adoption of dependencies and prerequisites. |
| RemoveLowPathwayCounts |
This BioModule set low Pathway counts below a configured threshold to zero.
These low sample counts are assumed to be miscategorized or genomic contamination. |
| RemoveScarcePathwayCounts |
This BioModule removes scarce pathways not found in enough samples.
Each pathway must be found in a configurable percentage of samples to be retained. |