This package is born out of my own frustration to automate the genomic data retrieval process to create computationally reproducible scripts for large-scale genomics studies. Since I couldn’t find easy-to-use and fully reproducible software libraries that would allow others and me to write transparent and easy to reproduce code, I sat down and tried to implement a framework that would enable anyone to automate the genomic data retrieval process. Personally, I strongly support and believe in reproducible research, and I truly hope that this package might be useful to others as well and that it helps to promote reproducible research in genomics studies.
I happily welcome anyone who wishes to contribute to this project :) Just drop me an email.
The vastly growing number of sequenced genomes allows us to perform a new type of biological research. Using a comparative approach these genomes provide us with new insights on how biological information is encoded on the molecular level and how this information changes over evolutionary time.
The first step, however, of any genome based study is to retrieve genomes from databases. To automate the retrieval process on a meta-genomic scale, the
biomartr package provides useful interface functions for genomic sequence retrieval and functional annotation retrieval. The major aim of
biomartr is to facilitate computational reproducibility and large-scale handling of genomic data for (meta-)genomic analyses.
biomartr aims to provide users with an easy to use framework to obtain genome, proteome, CDS, GFF (annotation), genome assembly quality, and metagenome project data. Furthermore, an interface to the Ensembl Biomart database allows users to retrieve functional annotation for genomic loci. Users can download entire databases such as
NCBI Genbank, etc. as well as
ENSEMBLGENOMES with only one command.
biomartr package is designed to achieve the highest degree of computational reproducibility in genomics research.
Please cite the following paper when using
biomartr for your own research. This will allow me to continue working on this software tool and will motivate me to extend its functionality and usability in the next years. Many thanks in advance :)
Drost HG, Paszkowski J. Biomartr: genomic data retrieval with R. Bioinformatics (2017) 33(8): 1216-1217. doi:10.1093/bioinformatics/btw821.
biomartralso at OmicTools.
Please find all FAQs here.
I would be very happy to learn more about potential improvements of the concepts and functions provided in this package.
Furthermore, in case you find some bugs or need additional (more flexible) functionality of parts of this package, please let me know:
twitter: HajkDrost or email
For Bug Reports: Please send me an issue.
Getting Started with
Users can also read the tutorials within (RStudio) :
# source the biomartr package library(biomartr) # look for all tutorials (vignettes) available in the biomartr package # this will open your web browser browseVignettes("biomartr")
# install biomartr 0.5.2 source("http://bioconductor.org/biocLite.R") biocLite('biomartr')
Some bug fixes or new functionality will not be available on CRAN yet, but in the developer version here on GitHub. To download and install the most recent version of
# install the current version of biomartr on your system source("http://bioconductor.org/biocLite.R") biocLite("HajkD/biomartr")
The current status of the package as well as a detailed history of the functionality of each version of
biomartr can be found in the NEWS section.
meta.retrieval(): Perform Meta-Genome Retieval from NCBI of species belonging to the same kingdom of life or to the same taxonomic subgroup
meta.retrieval.all(): Perform Meta-Genome Retieval from NCBI of the entire kingdom of life
getMetaGenomes(): Retrieve metagenomes from NCBI Genbank
getMetaGenomeAnnotations(): Retrieve annotation *.gff files for metagenomes from NCBI Genbank
listMetaGenomes(): List available metagenomes on NCBI Genbank
getMetaGenomeSummary(): Helper function to retrieve the assembly_summary.txt file from NCBI genbank metagenomes
listGenomes(): List all genomes available on NCBI and ENSEMBL servers
listKingdoms(): list the number of available species per kingdom of life on NCBI and ENSEMBL servers
listGroups(): list the number of available species per group on NCBI and ENSEMBL servers
getKingdoms(): Retrieve available kingdoms of life
getGroups(): Retrieve available groups for a kingdom of life
is.genome.available(): Check Genome Availability NCBI and ENSEMBL servers
getGenome(): Download a specific genome stored on NCBI and ENSEMBL servers
getProteome(): Download a specific proteome stored on NCBI and ENSEMBL servers
getCDS(): Download a specific CDS file (genome) stored on NCBI and ENSEMBL servers
getRNA(): Download a specific RNA file stored on NCBI and ENSEMBL servers
getGFF(): Genome Annotation Retrieval from NCBI (
*.gff) and ENSEMBL (
getGTF(): Genome Annotation Retrieval (
*.gtf) from ENSEMBL servers
getRepeatMasker() :Repeat Masker TE Annotation Retrieval
getAssemblyStats(): Genome Assembly Stats Retrieval from NCBI
getKingdomAssemblySummary(): Helper function to retrieve the assembly_summary.txt files from NCBI for all kingdoms
getMetaGenomeSummary(): Helper function to retrieve the assembly_summary.txt files from NCBI genbank metagenomes
getSummaryFile(): Helper function to retrieve the assembly_summary.txt file from NCBI for a specific kingdom
getENSEMBLInfo(): Retrieve ENSEMBL info file
getGENOMEREPORT(): Retrieve GENOME_REPORTS file from NCBI
read_genome(): Import genomes as Biostrings or data.table object
read_proteome(): Import proteome as Biostrings or data.table object
read_cds(): Import CDS as Biostrings or data.table object
read_gff(): Import GFF file
read_rna(): Import RNA file
read_rm(): Import Repeat Masker output file
read_assemblystats(): Import Genome Assembly Stats File
listNCBIDatabases(): Retrieve a List of Available NCBI Databases for Download
download.database(): Download a NCBI database to your local hard drive
download.database.all(): Download a complete NCBI Database such as e.g.
NCBI nrto your local hard drive
biomart(): Main function to query the BioMart database
getMarts(): Retrieve All Available BioMart Databases
getDatasets(): Retrieve All Available Datasets for a BioMart Database
getAttributes(): Retrieve All Available Attributes for a Specific Dataset
getFilters(): Retrieve All Available Filters for a Specific Dataset
organismBM(): Function for organism specific retrieval of available BioMart marts and datasets
organismAttributes(): Function for organism specific retrieval of available BioMart attributes
organismFilters(): Function for organism specific retrieval of available BioMart filters
getGO(): Function to retrieve GO terms for a given set of genes
# On Windows, this won't work - see ?build_github_devtools install_github("HajkD/biomartr", build_vignettes = TRUE, dependencies = TRUE) # When working with Windows, first you need to install the # R package: rtools -> install.packages("rtools") # Afterwards you can install devtools -> install.packages("devtools") # and then you can run: devtools::install_github("HajkD/biomartr", build_vignettes = TRUE, dependencies = TRUE) # and then call it from the library library("biomartr", lib.loc = "C:/Program Files/R/R-3.1.1/library")
biomartron a Win 8 laptop: solution ( Thanks to Andres Romanowski )
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.