disgenet2r is an R package to query and expand DisGeNET data (www.disgenet.org), and to visualize the results within R framework. The disgenet2r is designed to query data for DisGeNET v7.0 (May, 2020).

This report is used for package distribution and testing until it is ready to be published in BioConductor.

• Version: 0.99.3
• Subversion: 20230223
• Authors: IBI group
• Maintainer: [email protected]

The package, disgenet2r can be installed using devtools from this repository:

library(devtools)
install_bitbucket("ibi_group/disgenet2r")

Before using the package, you will need to create a free DisGeNET account at http://disgenet.org/signup. Once you have completed the registration process, use the get_disgenet_api_key function to retrieve your API key.

library(disgenet2r)
disgenet_api_key <- get_disgenet_api_key(
                  email = "[email protected]", 
                  password = "myspwd" )

After retrieving the API key, run the line below so the key is available for all the disgenet2r functions.

Sys.setenv(DISGENET_API_KEY= disgenet_api_key)

The following lines show two examples of how DisGeNET can be queried using disgenet2r:

• Gene Query

library(disgenet2r)
gq <- gene2disease(gene = 3953, 
 vocabulary = "ENTREZ",
    database = "ALL", 
    score = c( 0.1,1)
)

• Disease Query

library(disgenet2r)
dq <- disease2gene(disease = "C0028754", 
    database = "ALL",
    score = c(0.3,1) 
)

A detailed documentation of the functions of the package is available at http://www.disgenet.org/disgenet2r.

Copyright (C) 2023 IBI group.

disgenet2r is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

disgenet2r is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Piñero, J., Ramírez-Anguita, J. M., Saüch-Pitarch, J., Ronzano, F., Centeno, E., Sanz, F., & Furlong, L. I. (2020). The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic acids research, 48(D1), D845-D855.