https://github.com/egonw/bridgedbr

BIoconductor R package for BridgeDb
https://github.com/egonw/bridgedbr

bioinformatics bridgedb identifiers

Last synced: 24 days ago
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BIoconductor R package for BridgeDb

• Host: GitHub
• URL: https://github.com/egonw/bridgedbr
• Owner: egonw
• Created: 2017-08-27T11:52:18.000Z (about 7 years ago)
• Default Branch: devel
• Last Pushed: 2023-09-12T05:17:36.000Z (about 1 year ago)
• Last Synced: 2023-10-26T08:59:53.469Z (about 1 year ago)
• Topics: bioinformatics, bridgedb, identifiers
• Language: R
• Homepage:
• Size: 8.45 MB
• Stars: 5
• Watchers: 3
• Forks: 9
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
[![BioC Release Build Status](http://bioconductor.org/shields/build/release/bioc/BridgeDbR.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/BridgeDbR/) - Bioconductor Release Build

[![BioC Dev Build Status](http://bioconductor.org/shields/build/devel/bioc/BridgeDbR.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/BridgeDbR/) - Bioconductor Dev Build

# BridgeDbR package

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, https://doi.org/10.1186/1471-2105-11-5

The DOI of this package is https://doi.org/10.18129/B9.bioc.BridgeDbR

The source code of this package is available from https://github.com/bridgedb/BridgeDbR

License: AGPL-3

Available from Bioconductor

===========================

To install this package, start R and enter:

```

install.packages("BiocManager")

BiocManager::install("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

========================

To compile and install the lastest version from GitHub, or to test your patches, use the following

commands:

    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("curl") # if not present already

    > install.packages("devtools") # if not present already

    > library(devtools)

    > install_github("bridgedb/BridgeDbR")

Dependencies

============

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

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