All functions |
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Main BioMart Query Function |
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Genomic Data Retrieval |
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Get directory to store back end files like kingdom summaries etc |
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Set directory to store back end files like kingdom summaries etc |
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Check whether an annotation file contains outlier lines |
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Download a NCBI Database to Your Local Hard Drive |
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Download all elements of an NCBI databse |
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List all available ENSEMBL divisions |
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Helper function to retrieve species information from the ENSEMBL API |
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Genome Assembly Stats Retrieval |
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Retrieve All Available Attributes for a Specific Dataset |
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A wrapper to all bio getters, selected with 'type' argument |
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Generic Bio data set extractor |
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Coding Sequence Retrieval |
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CDS retrieval of multiple species |
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Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker, AssemblyStats |
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Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker, AssemblyStats of multiple species |
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Retrieve All Available Datasets for a BioMart Database |
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Download sequence or annotation from ENSEMBL |
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Helper function for retrieving biological sequence files from ENSEMBL |
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Helper function for retrieving gtf files from ENSEMBL |
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Retrieve ENSEMBLGENOMES info file |
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Retrieve ENSEMBL info file |
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Retrieve All Available Filters for a Specific Dataset |
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Retrieve NCBI GENOME_REPORTS file |
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Genome Annotation Retrieval (GFF3) |
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GFF retrieval of multiple species |
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Gene Ontology Query |
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Genome Annotation Retrieval (GTF) |
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Genome Retrieval |
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Genome Retrieval of multiple species |
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Retrieve available groups for a kingdom of life (only available for NCBI RefSeq and NCBI Genbank) |
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Retrieve and summarise the assembly_summary.txt files from NCBI for all kingdoms |
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Retrieve available kingdoms of life |
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Retrieve information about available Ensembl Biomart databases |
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Retrieve annotation *.gff files for metagenomes from NCBI Genbank |
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Retrieve the assembly_summary.txt file from NCBI genbank metagenomes |
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Retrieve metagenomes from NCBI Genbank |
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Proteome Retrieval |
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Proteome retrieval of multiple species |
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RNA Sequence Retrieval |
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RNA Retrieval of multiple species |
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Retrieve available database releases or versions of ENSEMBL |
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Repeat Masker Retrieval |
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Helper function to retrieve the assembly_summary.txt file from NCBI |
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Get uniprot info from organism |
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Retrieve UniProt Database Information File (STATS) |
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Check Genome Availability |
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Retrieve a List of Available NCBI Databases for Download |
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List All Available Genomes either by kingdom, group, or subgroup |
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List number of available genomes in each taxonomic group |
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List number of available genomes in each kingdom of life |
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List available metagenomes on NCBI Genbank |
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Perform Meta-Genome Retrieval |
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Perform Meta-Genome Retrieval of all organisms in all kingdoms of life |
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Retrieve Ensembl Biomart attributes for a query organism |
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Retrieve Ensembl Biomart marts and datasets for a query organism |
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Retrieve Ensembl Biomart filters for a qyery organism |
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Import Genome Assembly Stats File |
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Import CDS as Biostrings or data.table object |
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Import Genome Assembly as Biostrings or data.table object |
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Import GFF File |
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Import Proteome as Biostrings or data.table object |
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Import Repeat Masker output file |
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Import RNA as Biostrings or data.table object |
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Retrieve All Organism Names Stored on refseq |
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Retrieve summary statistics for a coding sequence (CDS) file |
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Retrieve summary statistics for a genome assembly file |