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
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
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")
This package requires RCurl and RJava, which can be installed with:
install.packages(pkgs=c("rJava", "RCurl"))