biocPkgList: Get full Bioconductor software package listing, with details

In seandavi/BiocPkgTools: Collection of simple tools for learning about Bioconductor Packages

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 = c("BioCsoft", "BioCexp", "BioCworkflows", "BioCann", "CRAN"),
  addBiocViewParents = TRUE
)

Arguments

version	The requested Bioconductor version. Will default to use the BiocManager defaults (i.e., version()).
repo	character(1) The requested Bioconductor repository. The default is to pull from the "BioCsoft" repository. Possible repositories include "BioCsoft", "BioCexp", "BioCworkflows", "BioCann", and "CRAN". Note that not all repos are available for all versions, particularly older versions.
addBiocViewParents	logical(1) 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(repo = "BioCsoft")
bpkgl
unlist(bpkgl[1,'Depends'], use.names = FALSE)

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

seandavi/BiocPkgTools documentation built on April 28, 2024, 1:31 p.m.