Main BioMart Query Function
Genomic Data Retrieval
Check whether an annotation file contains outlier lines
Format 'meta.retrieval' output
Download a NCBI Database to Your Local Hard Drive
Download all elements of an NCBI databse
Genome Assembly Stats Retrieval
Retrieve All Available Attributes for a Specific Dataset
Coding Sequence Retrieval
CDS retrieval of multiple species
Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker, AssemblyStats
Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker, AssemblyStats of multiple species
Retrieve All Available Datasets for a BioMart Database
Helper function for retrieving biological sequence files from ENSEMBL
Helper function for retrieving gff files from ENSEMBL
Retrieve ENSEMBLGENOMES info file
Retrieve ENSEMBL info file
Retrieve All Available Filters for a Specific Dataset
Retrieve NCBI GENOME_REPORTS file
Genome Annotation Retrieval (GFF3)
GFF retrieval of multiple species
Gene Ontology Query
Genome Annotation Retrieval (GTF)
Genome Retrieval
Genome Retrieval of multiple species
Retrieve available groups for a kingdom of life (only available for NCBI RefSeq and NCBI Genbank)
Retrieve and summarise the assembly_summary.txt files from NCBI for all kingdoms
Retrieve available kingdoms of life
Retrieve information about available Ensembl Biomart databases
Retrieve annotation *.gff files for metagenomes from NCBI Genbank
Retrieve the assembly_summary.txt file from NCBI genbank metagenomes
Retrieve metagenomes from NCBI Genbank
Proteome Retrieval
Proteome retrieval of multiple species
RNA Sequence Retrieval
RNA Retrieval of multiple species
Retrieve available database releases or versions of ENSEMBL
Repeat Masker Retrieval
Helper function to retrieve the assembly_summary.txt file from NCBI
Check Genome Availability
Retrieve a List of Available NCBI Databases for Download
List All Available Genomes either by kingdom, group, or subgroup
List number of available genomes in each taxonomic group
List number of available genomes in each kingdom of life
List available metagenomes on NCBI Genbank
Perform Meta-Genome Retrieval
Perform Meta-Genome Retrieval of all organisms in all kingdoms of life
Retrieve Ensembl Biomart attributes for a query organism
Retrieve Ensembl Biomart marts and datasets for a query organism
Retrieve Ensembl Biomart filters for a qyery organism
Import Genome Assembly Stats File
Import CDS as Biostrings or data.table object
Import Genome Assembly as Biostrings or data.table object
Import GFF File
Import Proteome as Biostrings or data.table object
Import Repeat Masker output file
Import RNA as Biostrings or data.table object
Retrieve All Organism Names Stored on refseq
Retrieve summary statistics for a coding sequence (CDS) file
Retrieve summary statistics for a genome assembly file