Genomic Data Retrieval
Check Genome Availability
Retrieve a List of Available NCBI Databases for Download
Main BioMart Query Function
Genomic Data Retrieval
Get directory to store back end files like kingdom summaries etc
Set directory to store back end files like kingdom summaries etc
Check whether an annotation file contains outlier lines
Download all elements of an NCBI databse
Download a NCBI Database to Your Local Hard Drive
List all available ENSEMBL divisions
Helper function to retrieve species information from the ENSEMBL API
Genome Assembly Stats Retrieval
Retrieve All Available Attributes for a Specific Dataset
A wrapper to all bio getters, selected with 'type' argument
Generic Bio data set extractor
Coding Sequence Retrieval
CDS retrieval of multiple species
Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker,...
Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker,...
Retrieve All Available Datasets for a BioMart Database
Helper function for retrieving gtf files from ENSEMBL
Download sequence or annotation from ENSEMBL
Helper function for retrieving biological sequence files from ENSEMBL
Retrieve ENSEMBLGENOMES info file
Retrieve ENSEMBL info file
Retrieve All Available Filters for a Specific Dataset
Genome Retrieval
Retrieve NCBI GENOME_REPORTS file
Genome Retrieval of multiple species
Genome Annotation Retrieval (GFF3)
GFF retrieval of multiple species
Gene Ontology Query
Retrieve available groups for a kingdom of life (only available for NC...
Genome Annotation Retrieval (GTF)
Retrieve and summarise the assembly_summary.txt files from NCBI for al...
Retrieve available kingdoms of life
Retrieve information about available Ensembl Biomart databases
Retrieve annotation *.gff files for metagenomes from NCBI Genbank
Retrieve metagenomes from NCBI Genbank
Retrieve the assembly_summary.txt file from NCBI genbank metagenomes
Proteome Retrieval
Proteome retrieval of multiple species
Retrieve available database releases or versions of ENSEMBL
Repeat Masker Retrieval
RNA Sequence Retrieval
RNA Retrieval of multiple species
Helper function to retrieve the assembly_summary.txt file from NCBI
Get uniprot info from organism
Retrieve UniProt Database Information File (STATS)
List All Available Genomes either by kingdom, group, or subgroup
List number of available genomes in each taxonomic group
List number of available genomes in each kingdom of life
List available metagenomes on NCBI Genbank
Perform Meta-Genome Retrieval of all organisms in all kingdoms of life
Perform Meta-Genome Retrieval
Retrieve Ensembl Biomart attributes for a query organism
Retrieve Ensembl Biomart marts and datasets for a query organism
Retrieve Ensembl Biomart filters for a query organism
Import Genome Assembly Stats File
Import CDS as Biostrings or data.table object
Import Genome Assembly as Biostrings or data.table object
Import GFF File
Import Proteome as Biostrings or data.table object
Import Repeat Masker output file
Import RNA as Biostrings or data.table object
Retrieve All Organism Names Stored on refseq
Retrieve summary statistics for a coding sequence (CDS) file
Retrieve summary statistics for a genome assembly file
Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.
Useful links