Bioconductor is an R package repository specialised in bioinformatics, as the name suggests. One unusual thing about it is its concept of periodic releases; each Bioconductor release contains a collection of packages in set versions.
Packages
First Bioconductor releases didn’t have that many packages; for example, Bioconductor 1.8 had 172 packages. Now (as of January 2025), the number of packages is more than 2000, which is about 1/10th of what CRAN contains.
wood_bioc_packages() |>
# There isn't enough space to list 2000+ packages.
print(max = 15)
#> [1] "a4" "a4Base" "a4Classif" "a4Core" "a4Preproc"
#> [6] "a4Reporting" "ABarray" "abseqR" "ABSSeq" "acde"
#> [11] "ACE" "aCGH" "ACME" "ADaCGH2" "ADAM"
#> [ reached getOption("max.print") -- omitted 2216 entries ]Available package version
As mentioned earlier, each Bioconductor release has a single package
version associated with it. To check version for any supported
Bioconductor release the user should use
wood_bioc_version().
wood_bioc_version("Biobase", release = "2.10")
#> [1] "2.16.0"Package dependencies
To list package dependencies the user should use
wood_bioc_dependencies(). This function extracts
dependencies from the DESCRIPTION file. By default the
package from the latest Bioconductor release is inspected (the same
behaviour can be obtained using release = "release"
parameter) but any release starting from 1.8 is supported, as long as
the package was included in said release.
wood_bioc_dependencies("Biobase")
#> <dependencies>
#> Depends: R (>= 2.10)
#> Depends: BiocGenerics (>= 0.27.1)
#> Depends: utils
#> Imports: methods
#> Suggests: tools
#> Suggests: tkWidgets
#> Suggests: ALL
#> Suggests: RUnit
#> Suggests: golubEsets
#> Suggests: BiocStyle
#> Suggests: knitr
#> Suggests: limma
wood_bioc_dependencies("Biobase", release = "2.10")
#> <dependencies>
#> Depends: R (>= 2.10)
#> Depends: utils
#> Depends: BiocGenerics (>= 0.1.0)
#> Imports: methods
#> Imports: BiocGenerics
#> Suggests: tools
#> Suggests: tkWidgets
#> Suggests: ALLBioconductor releases
The release parameter of all the other Bioconductor
functions accepts any valid Bioconductor release code, as well as
"release" and "devel" for the current and the
upcoming release respectively. To get the list of all named releases
(including releases 1.0 through 1.7, which are not supported yet due to
their data not being available) the user should use
wood_bioc_releases().
wood_bioc_releases()
#> [1] "3.20" "3.19" "3.18" "3.17" "3.16" "3.15" "3.14" "3.13" "3.12" "3.11"
#> [11] "3.10" "3.9" "3.8" "3.7" "3.6" "3.5" "3.4" "3.3" "3.2" "3.1"
#> [21] "3.0" "2.14" "2.13" "2.12" "2.11" "2.10" "2.9" "2.8" "2.7" "2.6"
#> [31] "2.5" "2.4" "2.3" "2.2" "2.1" "2.0" "1.9" "1.8" "1.7" "1.6"
#> [41] "1.5" "1.4" "1.3" "1.2" "1.1" "1.0"