https://github.com/jokergoo/uniprotkeywords
Keywords from the UniProt database
https://github.com/jokergoo/uniprotkeywords
Last synced: 3 months ago
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Keywords from the UniProt database
- Host: GitHub
- URL: https://github.com/jokergoo/uniprotkeywords
- Owner: jokergoo
- License: other
- Created: 2022-06-27T18:32:21.000Z (almost 3 years ago)
- Default Branch: master
- Last Pushed: 2023-09-23T07:28:59.000Z (over 1 year ago)
- Last Synced: 2025-01-28T16:34:33.219Z (5 months ago)
- Language: R
- Homepage: https://jokergoo.github.io/UniProtKeywords/
- Size: 20.6 MB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS
- License: LICENSE
Awesome Lists containing this project
README
# Keywords from the UniProt database
UniProt database provides a list of controlled vocabulary represented as keywords
for genes or proteins (https://www.uniprot.org/keywords/). This is useful for summarizing gene functions in a compact way. This package
provides data of keywords hierarchy and gene-keywords relations.
### Install
If you want the latest version, install it directly from GitHub:
```r
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("jokergoo/UniProtKeywords")
```
### Usage
First load the package:
```r
library(UniProtKeywords)
```
The package has five data objects. The first contains basic information of every keyword term:
```r
data(kw_terms)
kw_terms[["Cell cycle"]]
```
The other four contain hierarchical structures of the keyword terms:
```r
data(kw_parents)
kw_parents[1:2]
data(kw_children)
kw_children[1:2]
data(kw_ancestors)
kw_ancestors[1:2]
data(kw_offspring)
kw_offspring[1:2]
```
The **UniProtKeywords** package has also compiled genesets of keywords for some species, which can get by the function `load_keyword_genesets()`.
The argument is the taxon ID of a species:
```r
gl = load_keyword_genesets(9606)
gl[1:2]
```
### License
MIT @ Zuguang Gu