| Title: | Retrieve Disease-Related Genes from Public Sources |
|---|---|
| Description: | For researchers to quickly and comprehensively acquire disease genes, so as to understand the mechanism of disease, we developed this program to acquire disease-related genes. The data is integrated from three public databases. The three databases are 'eDGAR', 'DrugBank' and 'MalaCards'. The 'eDGAR' is a comprehensive database, containing data on the relationship between disease and genes. 'DrugBank' contains information on 13443 drugs and 5157 targets. 'MalaCards' integrates human disease information, including disease-related genes. |
| Authors: | Jiawei Wu [aut, cre], Xu Li [aut] |
| Maintainer: | Jiawei Wu <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 0.1.0 |
| Built: | 2025-03-01 05:20:51 UTC |
| Source: | https://github.com/cran/Autoseed |
Get disease-related genes from eDGAR, DrugBank and MalaCards
AutoSeed(search)AutoSeed(search)
search |
Name of the disease |
result$edgar: Containing Disease Name, OMIM ID and Genesymbol (Data comes from the eDGAR) result$malacards: Containing genes related to the disease (Data comes from the MalaCards) result$drugbank: Containing genes related to the disease (Data comes from the DrugBank)
result = AutoSeed("diabetes")result = AutoSeed("diabetes")
The data was collected in the drugbank. We got 27728 relationships between various disease and their related genes.
data("drugbank")data("drugbank")
A data frame with 27728 observations on the following 2 variables.
There are two columns in the data. The first column is genes and the second column is diseases.
<https://www.drugbank.ca/>
data(drugbank)data(drugbank)
Get disease-related genes from DrugBank.
drugbank_disease_gene(search)drugbank_disease_gene(search)
search |
Name of the disease, character |
The genes related to the disease, list
result = drugbank_disease_gene("diabetes")result = drugbank_disease_gene("diabetes")
The function "edgar_disease_gene()" will generate the relationship between gene and disease depend on this dataset.
data("edgar")data("edgar")
A data frame with 1038340 observations on the following 2 variables.
We got a total of 1038340 diseases and genes. There are two columns in the data. The first column is genes and the second column is diseases.
<http://edgar.biocomp.unibo.it/gene_disease_db/>
data(edgar)data(edgar)
Get disease-related genes from eDGAR
edgar_disease_gene(disease)edgar_disease_gene(disease)
disease |
Name of the disease, character |
a vector containing genesymbol related to the disease
result = edgar_disease_gene("diabetes")result = edgar_disease_gene("diabetes")
The data was collected in the Malacards. We got 241306 relationships between various disease and their related genes.
data("mala")data("mala")
A data frame with 241306 observations on the following 2 variables.
We got a total of 241306 diseases and genes. There are two columns in the data. The first column is disease and the second column is gene.
<https://doi.org/10.1093/nar/gkw1012>
data(mala)data(mala)
Get disease-related genes from MalaCards
malacards_disease_gene(disease)malacards_disease_gene(disease)
disease |
Name of the disease |
The genes related to the disease, character vector
result = malacards_disease_gene("diabetes")result = malacards_disease_gene("diabetes")