macros: Link to packages on Bioconductor, CRAN and GitHub

In BiocStyle: Standard styles for vignettes and other Bioconductor documents

Description

Functions for adding links to Bioconductor, CRAN and GitHub packages into R Markdown documents.

Usage

Biocpkg(pkg, vignette = NULL, label = NULL)

Biocbook(pkg, label = NULL)

Biocannopkg(pkg)

Biocexptpkg(pkg)

CRANpkg(pkg)

Rpackage(pkg)

Githubpkg(repo, pkg)

Arguments

pkg	character(1), package name
vignette	character(1), basename of vignette link, including html or pdf extension, e.g., "work-0-intro.html".
label	character(1) label used to identify the package or vignette. If NULL, defaults to pkg.
repo	Repository address in the format username/repo[/subdir]

Details

Use Biocpkg for Bioconductor software, annotation, experiment data, and workflow packages. When vignette=NULL, the function automatically includes a link to the package landing page, the version of which depends on the current Bioconductor version (i.e. if run in a devel environment, it will point towards the devel landing page; otherwise it will point to the release landing page).

Use Biocbook for Bioconductor webbooks. This will create a link to the index page of the book rather than to the landing page of the package used for the book's deployment.

Use CRANpkg for R packages available on CRAN. The function automatically includes a link to the master CRAN landing page.

Use Githubpkg for R packages available on GitHub. The repo should include the repository address in the format username/repo[/subdir]. If package is missing, the package name is assumed to be equal the repository name and is extracted from repo.

For R packages which are not available on Bioconductor, CRAN or GitHub, use Rpackage.

Value

Markdown-formatted character vector containing a hyperlinked package name. If vignette != NULL, the address of the specified vignette is returned.

Author(s)

Andrzej Oleś <[e-mail]>, 2014-2015

Examples

## link to a Bioconductor software package
Biocpkg("IRanges")

## link to a Bioconductor annotation package
Biocpkg("org.Mm.eg.db")

## link to a Bioconductor experiment data package
Biocpkg("affydata")

## link to a Bioconductor workflow
Biocpkg("simpleSingleCell")
Biocpkg(
    "simpleSingleCell",
    vignette = "work-0-intro.html",
    label = "Episode 1: analyzing scRNA-seq data with R/Bioconductor"
)

## link to a CRAN package
CRANpkg("data.table")

## link to an R package on GitHub
Githubpkg("rstudio/rmarkdown")

BiocStyle documentation built on Nov. 26, 2020, 2:01 a.m.