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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 query 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