biomartr

Functional Annotation and Biological Data Retrieval with R

The biomartr package aims to provide users with an easy to use framework to obtain genome, proteome, and CDS data, as well as an interface to BioMart to retrieve functional annotation. Furthermore, it is specifically designed to serve as additional module to the myTAI and orthologr frameworks, allowing the highest degree of reproducibility in evolutionary transcriptomics research from data retrieval to data visualization.

Additionally, the biomartr package allows users to retrieve entire NCBI databases using only one command (see Database Retrieval Vignette).

Installation

Before users can download and install biomartr they need to install the following packages from Bioconductor:

# install Bioconductor base packages
source("http://bioconductor.org/biocLite.R")
biocLite()

# load the biomaRt package
source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")

# load the Biostrings package
source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")

Users might be asked during the installation process of Biostrings and biomaRt whether or not they would like to update all package dependencies of the corresponding packages. Please type a specifying that all package dependencies of the corresponding packages shall be updated. This is important for the sufficient functionality of biomartr.

Now users can download biomartr from CRAN :

# install biomartr 0.0.3 from CRAN
install.packages("biomartr",
                 repos        = "https://cran.rstudio.com/",
                 dependencies = TRUE)

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.

Download Developer Version

The developer version of biomartr might include more functionality than the stable version on CRAN.

On Unix Based Systems

Now you can use the devtools package to install biomartr from GitHub.

# install.packages("devtools")

# install the current version of biomartr on your system
library(devtools)
install_github("HajkD/biomartr", build_vignettes = TRUE, dependencies = TRUE)

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

• Install biomartr on a Win 8 laptop: solution ( Thanks to Andres Romanowski )

Tutorials

Getting Started with biomartr:

• Introduction
• NCBI Database Retrieval
• Sequence and Database Retrieval
• Functional Annotation
• Phylotranscriptomics using myTAI, orthologr, and biomartr

BioMart Queries

• 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

Biological Data Retrieval

Genome Retrieval

• getGenome() : Download a specific genome stored on the NCBI ftp:// server
• listGenomes() : List all genomes available on the NCBI ftp:// server
• is.genome.available() : Check Genome Availability
• getProteome() : Download a specific proteome stored on the NCBI ftp:// server
• getCDS() : Download a specific CDS file (genome) stored on the NCBI ftp:// server

Database Retrieval

• listDatabases() : Retrieve a List of Available Databases for Download
• download_database() : Download a Database to Your Local Hard Drive

Performing Gene Ontology queries

Gene Ontology

• getGO() : Function to retrieve GO terms for a given set of genes

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 Report: Please send me an issue.