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.
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=\"\">4609</a>"link_entrez("4609", text = "this gene")## "<a href=\"\">this gene</a>"link_entrez("4609", text = "this gene", format = "markdown")## "[this gene]()"
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 ⇣
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
or the development version from GitHub with
definitiongene ontology data tags