qpmnguyen / TaxaSetsUtils

R package providing utilities for working with taxonomic sets for microbiome data

TaxaSetsUtils: Additional convenience functions to use taxonomic sets for microbiome analysis

This package provides utility functions to work with microbe sets. Some current (or planned) features:

• Attaching NCBI ids to taxonomic tables using both conventional name queries as well as via lookups tables (e.g. for databases such as SILVA and ChocoPhlAn)
• Use more complex path-matching approaches (e.g. Balvocuiute & Huson)
• Generate complementary BiocSet based on the dataset identifier (e.g. taxa_names in phyloseq) if multiple OTUs/ASVs are matched to the same genus/species.
• Attach sets from prepared ontologies such as BugSigDB