disgenet2r

This is fork of an old version, new versions can be found here

https://gitlab.com/medbio/disgenet2r

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).

What is this repository for?

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

Package' Status

Version: 0.99.3
Subversion: 20230223
Authors: IBI group
Maintainer: support@disgenet.org

How to start

Installation

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

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

Obtaining the API key

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 = "user@gmail.com", 
                  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)

Querying DisGeNET:

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

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/.

How to cite disgenet2r:

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.

jinfar / disgenet2r