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Type: Package
Title: Retrieve Disease-Related Genes from Public Sources
Version: 0.1.0
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.
Depends: R (≥ 3.5.0)
LazyData: TRUE
License: GPL (≥ 3)
Encoding: UTF-8
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-04-24 06:34:09 UTC; tsl-wujiawei
Author: Jiawei Wu [aut, cre], Xu Li [aut]
Maintainer: Jiawei Wu <jared_wood@163.com>
Repository: CRAN
Date/Publication: 2020-04-24 09:40:02 UTC

Get disease-related genes from eDGAR, DrugBank and MalaCards

Description

Get disease-related genes from eDGAR, DrugBank and MalaCards

Usage

AutoSeed(search)

Arguments

search

Name of the disease

Value

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)

Examples

result = AutoSeed("diabetes")

Relationship between gene and disease

Description

The data was collected in the drugbank. We got 27728 relationships between various disease and their related genes.

Usage

data("drugbank")

Format

A data frame with 27728 observations on the following 2 variables.

Details

There are two columns in the data. The first column is genes and the second column is diseases.

Source

<https://www.drugbank.ca/>

Examples

data(drugbank)

Get disease-related genes from DrugBank.

Description

Get disease-related genes from DrugBank.

Usage

drugbank_disease_gene(search)

Arguments

search

Name of the disease, character

Value

The genes related to the disease, list

Examples

result = drugbank_disease_gene("diabetes")

Relationship between the gene and disease in edgar

Description

The function "edgar_disease_gene()" will generate the relationship between gene and disease depend on this dataset.

Usage

data("edgar")

Format

A data frame with 1038340 observations on the following 2 variables.

Details

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.

Source

<http://edgar.biocomp.unibo.it/gene_disease_db/>

Examples

data(edgar)

Get disease-related genes from eDGAR

Description

Get disease-related genes from eDGAR

Usage

edgar_disease_gene(disease)

Arguments

disease

Name of the disease, character

Value

a vector containing genesymbol related to the disease

Examples

result = edgar_disease_gene("diabetes")

The relationship between gene and disease

Description

The data was collected in the Malacards. We got 241306 relationships between various disease and their related genes.

Usage

data("mala")

Format

A data frame with 241306 observations on the following 2 variables.

Details

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.

Source

<https://doi.org/10.1093/nar/gkw1012>

Examples

data(mala)

Get disease-related genes from MalaCards

Description

Get disease-related genes from MalaCards

Usage

malacards_disease_gene(disease)

Arguments

disease

Name of the disease

Value

The genes related to the disease, character vector

Examples

result = malacards_disease_gene("diabetes")

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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