biomartr

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Genomic Data Retrieval with R

Motivation:

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.

Short package description:

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.

In detail, 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 RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc. as well as ENSEMBL and ENSEMBLGENOMES with only one command.

Hence, the biomartr package is designed to achieve the highest degree of computational reproducibility in genomics research.

Citation

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.

Platforms

Find biomartr also at OmicTools.

Frequently Asked Questions (FAQs)

Please find all FAQs here.

Discussions and Bug Reports

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.

Tutorials

Getting Started with biomartr:

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")

Installation

# install biomartr 0.5.2
source("http://bioconductor.org/biocLite.R")
biocLite('biomartr')

Install Developer Version

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 biomartr run:

# install the current version of biomartr on your system
source("http://bioconductor.org/biocLite.R")
biocLite("HajkD/biomartr")

NEWS

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.

Genomic Data Retrieval

Meta-Genome Retrieval

Genome Retrieval

Import Downloaded Files

Database Retrieval

BioMart Queries

Performing Gene Ontology queries

Gene Ontology

Download Developer Version On Windows Systems

# 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")

Troubleshooting on Windows Machines

Code of conduct

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.