biomart | Main BioMart Query Function |
biomartr-package | Genomic Data Retrieval |
cachedir | Get directory to store back end files like kingdom summaries... |
cachedir_set | Set directory to store back end files like kingdom summaries... |
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 |
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,... |
getCollectionSet | Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF,... |
getDatasets | Retrieve All Available Datasets for a BioMart Database |
getENSEMBL | Download sequence or annotation from ENSEMBL |
getENSEMBLGENOMESInfo | Retrieve ENSEMBLGENOMES info file |
getENSEMBL.gtf | Helper function for retrieving gtf files from ENSEMBL |
get.ensembl.info | Helper function to retrieve species information from the... |
getENSEMBLInfo | Retrieve ENSEMBL info file |
getENSEMBL.Seq | Helper function for retrieving biological sequence files from... |
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... |
getGTF | Genome Annotation Retrieval (GTF) |
getKingdomAssemblySummary | Retrieve and summarise the assembly_summary.txt files from... |
getKingdoms | Retrieve available kingdoms of life |
getMarts | Retrieve information about available Ensembl Biomart... |
getMetaGenomeAnnotations | Retrieve annotation *.gff files for metagenomes from NCBI... |
getMetaGenomes | Retrieve metagenomes from NCBI Genbank |
getMetaGenomeSummary | Retrieve the assembly_summary.txt file from NCBI genbank... |
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... |
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... |
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... |
organismAttributes | Retrieve Ensembl Biomart attributes for a query organism |
organismBM | Retrieve Ensembl Biomart marts and datasets for a query... |
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 |
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