| biomart | Main BioMart Query Function |
| biomartr-package | Genomic Data Retrieval |
| cachedir | Get directory to store back end files like kingdom summaries... |
| cachedir_set | Set directory to store back end files like kingdom summaries... |
| check_annotation_biomartr | Check whether an annotation file contains outlier lines |
| download.database | Download a NCBI Database to Your Local Hard Drive |
| download.database.all | Download all elements of an NCBI databse |
| ensembl_divisions | List all available ENSEMBL divisions |
| getAssemblyStats | Genome Assembly Stats Retrieval |
| getAttributes | Retrieve All Available Attributes for a Specific Dataset |
| getBio | A wrapper to all bio getters, selected with 'type' argument |
| getBioSet | Generic Bio data set extractor |
| getCDS | Coding Sequence Retrieval |
| getCDSSet | CDS retrieval of multiple species |
| getCollection | Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF,... |
| getCollectionSet | Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF,... |
| getDatasets | Retrieve All Available Datasets for a BioMart Database |
| getENSEMBL | Download sequence or annotation from ENSEMBL |
| getENSEMBLGENOMESInfo | Retrieve ENSEMBLGENOMES info file |
| getENSEMBL.gtf | Helper function for retrieving gtf files from ENSEMBL |
| get.ensembl.info | Helper function to retrieve species information from the... |
| getENSEMBLInfo | Retrieve ENSEMBL info file |
| getENSEMBL.Seq | Helper function for retrieving biological sequence files from... |
| getFilters | Retrieve All Available Filters for a Specific Dataset |
| getGenome | Genome Retrieval |
| getGENOMEREPORT | Retrieve NCBI GENOME_REPORTS file |
| getGenomeSet | Genome Retrieval of multiple species |
| getGFF | Genome Annotation Retrieval (GFF3) |
| getGFFSet | GFF retrieval of multiple species |
| getGO | Gene Ontology Query |
| getGroups | Retrieve available groups for a kingdom of life (only... |
| getGTF | Genome Annotation Retrieval (GTF) |
| getKingdomAssemblySummary | Retrieve and summarise the assembly_summary.txt files from... |
| getKingdoms | Retrieve available kingdoms of life |
| getMarts | Retrieve information about available Ensembl Biomart... |
| getMetaGenomeAnnotations | Retrieve annotation *.gff files for metagenomes from NCBI... |
| getMetaGenomes | Retrieve metagenomes from NCBI Genbank |
| getMetaGenomeSummary | Retrieve the assembly_summary.txt file from NCBI genbank... |
| getProteome | Proteome Retrieval |
| getProteomeSet | Proteome retrieval of multiple species |
| getReleases | Retrieve available database releases or versions of ENSEMBL |
| getRepeatMasker | Repeat Masker Retrieval |
| getRNA | RNA Sequence Retrieval |
| getRNASet | RNA Retrieval of multiple species |
| getSummaryFile | Helper function to retrieve the assembly_summary.txt file... |
| getUniProtInfo | Get uniprot info from organism |
| getUniProtSTATS | Retrieve UniProt Database Information File (STATS) |
| is.genome.available | Check Genome Availability |
| listDatabases | Retrieve a List of Available NCBI Databases for Download |
| listGenomes | List All Available Genomes either by kingdom, group, or... |
| listGroups | List number of available genomes in each taxonomic group |
| listKingdoms | List number of available genomes in each kingdom of life |
| listMetaGenomes | List available metagenomes on NCBI Genbank |
| meta.retrieval | Perform Meta-Genome Retrieval |
| meta.retrieval.all | Perform Meta-Genome Retrieval of all organisms in all... |
| organismAttributes | Retrieve Ensembl Biomart attributes for a query organism |
| organismBM | Retrieve Ensembl Biomart marts and datasets for a query... |
| organismFilters | Retrieve Ensembl Biomart filters for a qyery 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 |
| read_rm | Import Repeat Masker output file |
| read_rna | Import RNA as Biostrings or data.table object |
| refseqOrganisms | Retrieve All Organism Names Stored on refseq |
| summary_cds | Retrieve summary statistics for a coding sequence (CDS) file |
| summary_genome | Retrieve summary statistics for a genome assembly file |
