Package index • amRdata

All functions
`CDHIT2duckdb()`	Cluster proteins with CD-HIT and write results to DuckDB
`class_abbr`	Drug class abbreviations
`clean_drug`	Clean drug names
`cleaned_bvbrc_countries`	Cleaned BV-BRC country names
`domainFromIPR()`	Derive protein domain presence/absence and counts via InterProScan and write to DuckDB
`.extractAMRtable()`	Extract AMR Data Table
`.extractGenomeData()`	This function retrieves metadata for the given genome IDs.
`.filterGenomes()`	Filter genomes by AMR phenotype and metadata, and store results in DuckDB
`.generateDBname()`	Generate a shortened database name from taxon IDs or species names
`.getGenomeIDs()`	Retrieve genome IDs from BV-BRC and store them in DuckDB
`.retrieveCustomQuery()`	Retrieve BV-BRC records for user-provided bacteria
`.retrieveQueryIDs()`	Retrieve genome IDs for each taxon via BV-BRC and DuckDB
`.updateBVBRCdata()`	Update BV-BRC metadata in DuckDB
`drug_abbr`	Drug abbreviations
`drug_class`	Drug class mappings
`genomeList()`	Build a table of local genome file paths and write to DuckDB
`prepareGenomes()`	Download and prepare all files for a chosen bacterial species or TaxID
`retrieveGenomes()`	Download .fna, .faa, .gff files for filtered BV-BRC genomes
`retrieveMetadata()`	Retrieve AMR or Microtrait metadata from BV-BRC and store in DuckDB
`runDataProcessing()`	Run the full amRdata processing pipeline (Panaroo → CD-HIT → InterProScan → Parquet)
`runPanaroo2Duckdb()`	Run Panaroo and import pangenome outputs into DuckDB

Reference