Genomic Data Retrieval


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Documentation for package ‘biomartr’ version 0.9.2

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biomartr-package Genomic Data Retrieval
biomart Main BioMart Query Function
biomartr Genomic Data Retrieval
clean.retrieval Format 'meta.retrieval' output
download.database Download a NCBI Database to Your Local Hard Drive
download.database.all Download all elements of an NCBI databse
getAssemblyStats Genome Assembly Stats Retrieval
getAttributes Retrieve All Available Attributes for a Specific Dataset
getCDS Coding Sequence Retrieval
getCDSSet CDS retrieval of multiple species
getCollection Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker, AssemblyStats
getDatasets Retrieve All Available Datasets for a BioMart Database
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
is.genome.available Check Genome Availability
listDatabases Retrieve a List of Available NCBI Databases for Download
listGenomes List All Available Genomes
listGroups List number of available genomes in each 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 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