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 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")