Genomic Data Retrieval

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Documentation for package ‘biomartr’ version 1.0.7

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

biomartr-package	Genomic Data Retrieval
biomart	Main BioMart Query Function
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.gtf	Helper function for retrieving gtf files from ENSEMBL
getENSEMBL.Seq	Helper function for retrieving biological sequence files from ENSEMBL
getENSEMBLGENOMESInfo	Retrieve ENSEMBLGENOMES info file
getENSEMBLInfo	Retrieve ENSEMBL info file
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 available for NCBI RefSeq and NCBI Genbank)
getGTF	Genome Annotation Retrieval (GTF)
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
getMetaGenomes	Retrieve metagenomes from NCBI Genbank
getMetaGenomeSummary	Retrieve the assembly_summary.txt file from NCBI genbank metagenomes
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 from NCBI
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 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
listNCBIDatabases	Retrieve a List of Available NCBI Databases for Download
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