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.
character(1) or package_version indicating the
Bioconductor version (e.g., "3.22"). Defaults to the "current version"
provided by BiocManager::version(). The keywords "release" and "devel"
are also accepted.
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.
logical(1) whether to add all biocViews
parents to biocViews annotations.
An object of class tbl_df with one row per package. The result
always includes a fnd list-column whose elements are character vectors
of funder names extracted from persons with role "fnd" in the
formatted Author field. Elements are NA_character_ for packages
that declare no funder (or whose Author field contains no [fnd]
role tag).
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.
bpkgl <- biocPkgList(repo = "BioCsoft")
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://cran.rstudio.com
bpkgl
#> # A tibble: 2,418 × 48
#> Package Version Depends Suggests License MD5sum NeedsCompilation Title
#> <chr> <chr> <list> <list> <chr> <chr> <chr> <chr>
#> 1 a4 1.60.0 <chr [5]> <chr [7]> GPL-3 9e320… no "Aut…
#> 2 a4Base 1.60.0 <chr [2]> <chr [4]> GPL-3 e7fc4… no "Aut…
#> 3 a4Classif 1.60.0 <chr [2]> <chr [4]> GPL-3 07449… no "Aut…
#> 4 a4Core 1.60.0 <chr [1]> <chr [2]> GPL-3 839c3… no "Aut…
#> 5 a4Preproc 1.60.0 <chr [1]> <chr [4]> GPL-3 c3c7d… no "Aut…
#> 6 a4Reporting 1.60.0 <chr [1]> <chr [2]> GPL-3 20801… no "Aut…
#> 7 ABarray 1.80.0 <chr [1]> <chr [2]> GPL 95858… no "Mic…
#> 8 abseqR 1.30.0 <chr [1]> <chr [1]> GPL-3 … 934b6… no "Rep…
#> 9 ABSSeq 1.66.0 <chr [2]> <chr [1]> GPL (>… e84a3… no "ABS…
#> 10 acde 1.42.0 <chr [2]> <chr [2]> GPL-3 0ddff… no "Art…
#> # ℹ 2,408 more rows
#> # ℹ 40 more variables: Description <chr>, biocViews <list>, Author <list>,
#> # Maintainer <list>, git_url <chr>, git_branch <chr>, git_last_commit <chr>,
#> # git_last_commit_date <chr>, `Date/Publication` <chr>, source.ver <chr>,
#> # win.binary.ver <chr>, `mac.binary.big-sur-x86_64.ver` <chr>,
#> # `mac.binary.sonoma-arm64.ver` <chr>, vignettes <list>,
#> # vignetteTitles <list>, hasREADME <chr>, hasNEWS <chr>, hasINSTALL <chr>, …
unlist(bpkgl[1,'Depends'], use.names = FALSE)
#> [1] "a4Base" "a4Preproc" "a4Classif" "a4Core" "a4Reporting"
# Get a list of all packages that
# import "GEOquery"
library(dplyr)
#>
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#>
#> filter, lag
#> The following objects are masked from ‘package:base’:
#>
#> intersect, setdiff, setequal, union
bpkgl |>
filter(Package == 'GEOquery') |>
pull('importsMe') |>
unlist()
#> [1] "bigmelon" "ChIPXpress"
#> [3] "DExMA" "EGAD"
#> [5] "minfi" "Moonlight2R"
#> [7] "MoonlightR" "phantasus"
#> [9] "recount" "BeadArrayUseCases"
#> [11] "BioPlex" "GSE13015"
#> [13] "healthyControlsPresenceChecker" "geneExpressionFromGEO"
#> [15] "RCPA"