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