Man pages for HajkD/biomartr
Genomic Data Retrieval

biomartMain BioMart Query Function
biomartr-packageGenomic Data Retrieval
clean.retrievalFormat 'meta.retrieval' output
download.databaseDownload a NCBI Database to Your Local Hard Drive
download.database.allDownload all elements of an NCBI databse
getAssemblyStatsGenome Assembly Stats Retrieval
getAttributesRetrieve All Available Attributes for a Specific Dataset
getCDSCoding Sequence Retrieval
getCollectionRetrieve a Collection: Genome, Proteome, CDS, RNA, GFF,...
getDatasetsRetrieve All Available Datasets for a BioMart Database
getENSEMBLInfoRetrieve ENSEMBL info file
getFiltersRetrieve All Available Filters for a Specific Dataset
getGenomeGenome Retrieval
getGFFGenome Annotation Retrieval (GFF3)
getGOGene Ontology Query
getGroupsRetrieve available groups for a kingdom of life (only...
getGTFGenome Annotation Retrieval (GTF)
getKingdomAssemblySummaryRetrieve and summarise the assembly_summary.txt files from...
getKingdomsRetrieve available kingdoms of life
getMartsRetrieve information about available Ensembl Biomart...
getMetaGenomeAnnotationsRetrieve annotation *.gff files for metagenomes from NCBI...
getMetaGenomesRetrieve metagenomes from NCBI Genbank
getMetaGenomeSummaryRetrieve the assembly_summary.txt file from NCBI genbank...
getProteomeProteome Retrieval
getReleasesRetrieve available database releases or versions of ENSEMBL...
getRepeatMaskerRepeat Masker Retrieval
getRNARNA Sequence Retrieval
getSummaryFileHelper function to retrieve the assembly_summary.txt file...
is.genome.availableCheck Genome Availability
listDatabasesRetrieve a List of Available NCBI Databases for Download
listGenomesList All Available Genomes
listGroupsList number of available genomes in each group
listKingdomsList number of available genomes in each kingdom of life
listMetaGenomesList available metagenomes on NCBI Genbank
meta.retrievalPerform Meta-Genome Retrieval
meta.retrieval.allPerform Meta-Genome Retrieval of all organisms in all...
organismAttributesRetrieve Ensembl Biomart attributes for a query organism
organismBMRetrieve Ensembl Biomart marts and datasets for a query...
organismFiltersRetrieve Ensembl Biomart filters for a qyery organism
read_assemblystatsImport Genome Assembly Stats File
read_cdsImport CDS as Biostrings or data.table object
read_genomeImport Genome Assembly as Biostrings or data.table object
read_gffImport GFF File
read_proteomeImport Proteome as Biostrings or data.table object
read_rmImport Repeat Masker output file
read_rnaImport RNA as Biostrings or data.table object
refseqOrganismsRetrieve All Organism Names Stored on refseq
HajkD/biomartr documentation built on Aug. 15, 2018, 1:25 a.m.