Function reference • biomartr

# Reference

## All functions
`biomart()` | Main BioMart Query Function
`biomartr-package` `biomartr` | Genomic Data Retrieval
`cachedir()` | Get directory to store back end files like kingdom summaries etc
`cachedir_set()` | Set directory to store back end files like kingdom summaries etc
`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
`get.ensembl.info()` | Helper function to retrieve species information from the ENSEMBL API
`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, Repeat Masker, AssemblyStats
`getCollectionSet()` | Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker, AssemblyStats of multiple species
`getDatasets()` | Retrieve All Available Datasets for a BioMart Database
`getENSEMBL()` | Download sequence or annotation from ENSEMBL
`getENSEMBL.Seq()` | Helper function for retrieving biological sequence files from ENSEMBL
`getENSEMBL.gtf()` | Helper function for retrieving gtf files from ENSEMBL
`getENSEMBLGENOMESInfo()` | Retrieve ENSEMBLGENOMES info file
`getENSEMBLInfo()` | Retrieve ENSEMBL info file
`getFilters()` | Retrieve All Available Filters for a Specific Dataset
`getGENOMEREPORT()` | Retrieve NCBI GENOME_REPORTS file
`getGFF()` | Genome Annotation Retrieval (GFF3)
`getGFFSet()` | GFF retrieval of multiple species
`getGO()` | Gene Ontology Query
`getGTF()` | Genome Annotation Retrieval (GTF)
`getGenome()` | Genome Retrieval
`getGenomeSet()` | Genome Retrieval of multiple species
`getGroups()` | Retrieve available groups for a kingdom of life (only available for NCBI RefSeq and NCBI Genbank)
`getKingdomAssemblySummary()` | Retrieve and summarise the assembly_summary.txt files from NCBI for all kingdoms
`getKingdoms()` | Retrieve available kingdoms of life
`getMarts()` | Retrieve information about available Ensembl Biomart databases
`getMetaGenomeAnnotations()` | Retrieve annotation *.gff files for metagenomes from NCBI Genbank
`getMetaGenomeSummary()` | Retrieve the assembly_summary.txt file from NCBI genbank metagenomes
`getMetaGenomes()` | Retrieve metagenomes from NCBI Genbank
`getProteome()` | Proteome Retrieval
`getProteomeSet()` | Proteome retrieval of multiple species
`getRNA()` | RNA Sequence Retrieval
`getRNASet()` | RNA Retrieval of multiple species
`getReleases()` | Retrieve available database releases or versions of ENSEMBL
`getRepeatMasker()` | Repeat Masker Retrieval
`getSummaryFile()` | Helper function to retrieve the assembly_summary.txt file from NCBI
`getUniProtInfo()` | Get uniprot info from organism
`getUniProtSTATS()` | Retrieve UniProt Database Information File (STATS)
`is.genome.available()` | Check Genome Availability
`listDatabases()` `listNCBIDatabases()` | Retrieve a List of Available NCBI Databases for Download
`listGenomes()` | List All Available Genomes either by kingdom, group, or subgroup
`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 kingdoms of life
`organismAttributes()` | Retrieve Ensembl Biomart attributes for a query organism
`organismBM()` | Retrieve Ensembl Biomart marts and datasets for a query organism
`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