https://github.com/bioconductor-source/uniprotkeywords
Science Score: 13.0%
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○CITATION.cff file
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✓codemeta.json file
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○Scientific vocabulary similarity
Low similarity (6.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: other
- Language: R
- Default Branch: devel
- Size: 20.6 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
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(kwparents) kwparents[1:2]
data(kwchildren) kwchildren[1:2]
data(kwancestors) kwancestors[1:2]
data(kwoffspring) kwoffspring[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
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
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Dependencies
- R >= 4.0.0 depends
- utils * imports
- knitr * suggests
- markdown * suggests
- rmarkdown * suggests
- testthat * suggests