bridgedb-r

R package for BridgeDb, a tool for identifier mapping.

Learn about BridgeDb at http://www.bridgedb.org/ and read about it in this paper:

Van Iersel, M.; Pico, A.; Kelder, T.; Gao, J.; Ho, I.; Hanspers, K.; Conklin, B.; Evelo, C. BMC Bioinformatics 2010, 11, 5

The source code of this package is available from:

https://github.com/BiGCAT-UM/bridgedb-r

License: AGPL-3

Available from Bioconductor

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("BridgeDbR")

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BridgeDbR")

http://www.bioconductor.org/packages/release/bioc/html/BridgeDbR.html

Compiling and Installing

R CMD build BridgeDbR
R CMD check BridgeDbR_x.y.z.tar.gz
R CMD INSTALL BridgeDbR_x.y.z.tar.gz

To create the vignette:

rm -f BridgeDbR/inst/doc/tutorial.pdf; R CMD build BridgeDbR; tar xvf BridgeDbR_0.99.1.tar.gz BridgeDbR/inst/doc/tutorial.pdf

To install the packages from within R with the devtools package:

> install.packages("rJava") # if not present already
> install.packages("RCurl") # if not present already
> install.packages("devtools") # if not present already
> library(devtools)
> install_github("BiGCAT-UM/bridgedb-r", subdir="BridgeDbR")

Dependencies

This package requires RCurl and RJava, which can be installed with:

install.packages(pkgs=c("rJava", "RCurl"))