biomartr-package | Genomic Data Retrieval |
biomart | Main BioMart Query Function |
biomartr | Genomic Data Retrieval |
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 |
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 |
getGFF | Genome Annotation Retrieval (GFF3) |
getGO | Gene Ontology Query |
getGroups | Retrieve available groups for a kingdom of life |
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 |
getReleases | Retrieve available database releases or versions of ENSEMBL and ENSEMBLGENOMES |
getRepeatMasker | Repeat Masker Retrieval |
getRNA | RNA Sequence Retrieval |
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 |