biocPkgList {BiocPkgTools} | R Documentation

## Get full Bioconductor software package listing, with details

### Description

The BiocViews-generated `VIEWS` file is available for Bioconductor release and devel repositories. It contains quite a bit more information from the package `DESCRIPTION` files than the `PACKAGES` file. In particular, it contains `biocViews` annotations and URLs for vignettes and developer URLs.

### Usage

    biocPkgList(
      version = BiocManager::version(),
      repo = "BioCsoft",
      addBiocViewParents = TRUE
    )

### Arguments

`version` | The requested Bioconductor version. Will default to use the BiocManager defaults (ie., `version()`).
`repo` | The requested biooconductor repository. The default will be the Bioconductor software repository: BioCsoft. Available repos include: "BioCsoft", "BioCann", "BioCexp", "BioCworkflows", and "CRAN". Note that not all repos are available for all versions, particularly older versions (but who would use those, right?).
`addBiocViewParents` | logical(), whether to add all biocViews parents to biocViews annotations.

### Details

Since packages are annotated with the most specific views, the default functionality here is to add parent terms for all views for each package. For example, in the bioCsoft repository, all packages will have at least "Software" added to their biocViews. If one wants to stick to only the most specific terms, set `addBiocViewParents` to `FALSE`.

### Value

An object of class `tbl_df`.

### Examples

    bpkgl = biocPkgList()
    bpkgl
    unlist(bpkgl[1,'Depends'])

    # Get a list of all packages that
    # import "GEOquery"
    library(dplyr)
    bpkgl %>%
      filter(Package=='GEOquery') %>%
      pull(c('importsMe'))

[Package BiocPkgTools version 1.12.2 Index]