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:
Bold indicates support for data tags (see below).
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)"
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.
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.
Install the released version of biolink from CRAN
install.packages("biolink")
or the development version from GitHub with
# install.packages("devtools")
::install_github("aaronwolen/biolink") devtools