biolink v0.1.7

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Create Hyperlinks to Biological Databases and Resources

Generate urls and hyperlinks to commonly used biological databases and resources based on standard identifiers. This is primarily useful when writing dynamic reports that reference things like gene symbols in text or tables, allowing you to, for example, convert gene identifiers to hyperlinks pointing to their entry in the 'NCBI' Gene database. Currently supports 'NCBI' Gene, 'PubMed', Gene Ontology, 'KEGG', CRAN and Bioconductor.

Readme

biolink

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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 to request support for additional resources

Bold indicates support for data tags (see below).

Usage

Basic idea

link_entrez("4609")
## "<a href=\"https://www.ncbi.nlm.nih.gov/gene/4609\">4609</a>"

link_entrez("4609", text = "this gene")
## "<a href=\"https://www.ncbi.nlm.nih.gov/gene/4609\">this gene</a>"

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", "<symbol>")`.

⇣ generates ⇣

Note that this paper found that the ErbB signaling pathway (hsa04012) and response to organic substance process (GO:001003) are enriched for a network of oncogenes, including MYC.

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", "<symbol>") produces MYC 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

install.packages("biolink")

or the development version from GitHub with

# install.packages("devtools")
devtools::install_github("aaronwolen/biolink")

Functions in biolink

Name Description
build_link Construct hypertext links
biolink biolink makes it easy to link to online resources
links Construct hyperlinks to online resources
urls Construct urls to online resources
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Details

Type Package
License MIT + file LICENSE
Encoding UTF-8
LazyData true
RoxygenNote 7.1.1
NeedsCompilation no
Packaged 2020-10-26 16:41:12 UTC; aaronwolen
Repository CRAN
Date/Publication 2020-11-01 17:20:03 UTC

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