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| biomart | Main BioMart Query Function |
| download.database | Download a NCBI Database to Your Local Hard Drive |
| download.database.all | Download all elements of an NCBI databse |
| getAssemblyStats | Genome Assembly Stats Retrieval |
| getAttributes | Retrieve All Available Attributes for a Specific Dataset |
| getCDS | Coding Sequence Retrieval |
| getDatasets | Retrieve All Available Datasets for a BioMart Database |
| getENSEMBLGENOMESInfo | Retrieve ENSEMBLGENOMES info file |
| getENSEMBLInfo | Retrieve ENSEMBL info file |
| getFilters | Retrieve All Available Filters for a Specific Dataset |
| getGenome | Genome Retrieval |
| getGENOMEREPORT | Retrieve NCBI GENOME_REPORTS file |
| getGFF | Genome Annotation Retrieval |
| getGO | Gene Ontology Query |
| getGroups | Retrieve available groups for a kingdom of life |
| getKingdomAssemblySummary | Retrieve and summarise the assembly_summary.txt files from NCBI for all kingdoms |
| getKingdoms | Retrieve available kingdoms of life |
| getMarts | Retrieve All Available BioMart Databases |
| getMetaGenomeAnnotations | Retrieve annotation *.gff files for metagenomes from NCBI Genbank |
| getMetaGenomes | Retrieve metagenomes from NCBI Genbank |
| getMetaGenomeSummary | Retrieve the assembly_summary.txt file from NCBI genbank metagenomes |
| getProteome | Proteome Retrieval |
| getSummaryFile | Helper function to retrieve the assembly_summary.txt file from NCBI |
| is.genome.available | Check Genome Availability |
| listDatabases | Retrieve a List of Available NCBI Databases for Download |
| listGenomes | List All Available Genomes |
| listGroups | List number of available genomes in each group |
| listKingdoms | List number of available genomes in each kingdom of life |
| listMetaGenomes | List available metagenomes on NCBI Genbank |
| meta.retrieval | Perform Meta-Genome Retieval |
| meta.retrieval.all | Perform Meta-Genome Retieval of all organisms in all kingdoms of life |
| organismAttributes | Retrieve Biomart Attributes for an Organism |
| organismBM | Retrieve Biomart Marts and Datasets for an Organism |
| organismFilters | Retrieve Biomart Filters for an Organism |
| read_assemblystats | Import Genome Assembly Stats File |
| read_cds | Import CDS as Biostrings or data.table object |
| read_genome | Import Genome Assembly as Biostrings or data.table object |
| read_gff | Import GFF File |
| read_proteome | Import Proteome as Biostrings or data.table object |
| refseqOrganisms | Retrieve All Organism Names Stored on refseq |