https://github.com/aaronwolen/biolink
:link: R package for creating hyperlinks to biological databases and resources
https://github.com/aaronwolen/biolink
bioinformatics dynamic-documents r rmarkdown
Last synced: 7 months ago
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:link: R package for creating hyperlinks to biological databases and resources
- Host: GitHub
- URL: https://github.com/aaronwolen/biolink
- Owner: aaronwolen
- License: other
- Created: 2017-02-20T18:35:51.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2023-08-21T22:49:59.000Z (almost 3 years ago)
- Last Synced: 2025-02-01T20:45:00.345Z (over 1 year ago)
- Topics: bioinformatics, dynamic-documents, r, rmarkdown
- Language: R
- Homepage:
- Size: 104 KB
- Stars: 6
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
Awesome Lists containing this project
README
# biolink
[](https://cran.r-project.org/package=biolink)
[](https://cran.r-project.org/web/checks/check_results_biolink.html)
[](https://github.com/aaronwolen/biolink/actions)
[](https://app.codecov.io/github/aaronwolen/biolink?branch=master)
[](https://www.r-pkg.org/pkg/biolink)
biolink makes it easy to create hyperlinks to various online databases/resources for inclusion in dynamic reports written in Markdown, HTML or LaTeX.
It currently supports generating links for:
- **PubMed articles**
- **Gene Ontologies**
- Kegg Pathways
- **Entrez genes**
- R packages on CRAN or Bioconductor
- create an [issue](https://github.com/aaronwolen/biolink/issues) to request support for additional resources
**Bold** indicates support for *data tags* (see below).
## Usage
### Basic idea
```r
link_entrez("4609")
## "4609"
link_entrez("4609", text = "this gene")
## "this gene"
link_entrez("4609", text = "this gene", format = "markdown")
## "[this gene](https://www.ncbi.nlm.nih.gov/gene/4609)"
```
### Extended example
```
Note that `r link_pubmed("22952919", "this paper")` found that the ErbB
signaling pathway (`r link_kegg("hsa04012")`) and response to organic
substance process (`r link_go("GO:0010033")`) are enriched for a network
of oncogenes, including `r link_entrez("4609", "")`.
```
⇣ generates ⇣
> Note that [this paper][1] found that the ErbB signaling pathway ([hsa04012][2]) and response to organic substance process ([GO:001003][3]) are enriched for a network of oncogenes, including [MYC][4].
### Data tags
For a few supported resources, specially formatted tags can be used to retrieve data from the corresponding resource. In the example above, `link_entrez("4609", "")` produces [MYC][4] because the gene symbol was retrieved from NCBI.
See the package documentation for a complete list of supported data tags.
## Installation
Install the released version of biolink from CRAN
```R
install.packages("biolink")
```
or the development version from GitHub with
```R
# install.packages("devtools")
devtools::install_github("aaronwolen/biolink")
```
## See also
- [annotate](https://bioconductor.org/packages/annotate) from Bioconductor
[1]: https://pubmed.ncbi.nlm.nih.gov/22952919/
[2]: https://www.genome.jp/dbget-bin/www_bget?pathway:hsa04012
[3]: https://amigo.geneontology.org/amigo/term/GO:0010033
[4]: https://www.ncbi.nlm.nih.gov/gene/4609