Package index • biomartr

All functions

biomart(): Main BioMart Query Function

biomartr-package 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.Seq(): Helper function for retrieving biological sequence files from ENSEMBL

getENSEMBL.gtf(): Helper function for retrieving gtf files from ENSEMBL

getENSEMBLGENOMESInfo(): Retrieve ENSEMBLGENOMES info file

getENSEMBLInfo(): Retrieve ENSEMBL info file

getFilters(): Retrieve All Available Filters for a Specific Dataset

getGENOMEREPORT(): Retrieve NCBI GENOME_REPORTS file

getGFF(): Genome Annotation Retrieval (GFF3)

getGFFSet(): GFF retrieval of multiple species

getGO(): Gene Ontology Query

getGTF(): Genome Annotation Retrieval (GTF)

getGenome(): Genome Retrieval

getGenomeSet(): Genome Retrieval of multiple species

getGroups(): Retrieve available groups for a kingdom of life (only available for NCBI RefSeq and NCBI Genbank)

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

getMetaGenomeSummary(): Retrieve the assembly_summary.txt file from NCBI genbank metagenomes

getMetaGenomes(): Retrieve metagenomes from NCBI Genbank

getProteome(): Proteome Retrieval

getProteomeSet(): Proteome retrieval of multiple species

getRNA(): RNA Sequence Retrieval

getRNASet(): RNA Retrieval of multiple species

getReleases(): Retrieve available database releases or versions of ENSEMBL

getRepeatMasker(): Repeat Masker Retrieval

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() listNCBIDatabases(): 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

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