Look up a packages Bioconductor dependencies

The function uses the pkgType argument to restrict the look up to only the relevant Bioconductor repository. It works for multiple packages of the same type.

pkgBiocDeps(
  pkg,
  pkgType = c("software", "data-experiment", "workflows", "data-annotation"),
  which = "strong",
  only.bioc = TRUE,
  version = BiocManager::version()
)

Arguments

pkg

character(1) The name of a Bioconductor package

pkgType

character(1) Either one of 'software', 'data-experiment', 'workflows', or 'data-annotation' (defaults to 'all' or 'software')

which

a character vector listing the types of dependencies, a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances"). Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector.

only.bioc

logical(1) Whether to only return Bioconductor dependencies in the list (default TRUE)

version

(Optional) character(1) or package_version indicating the Bioconductor version (e.g., "3.8") for which repositories are required.

Examples

pkgBiocDeps("MultiAssayExperiment", only.bioc = TRUE)
#> $MultiAssayExperiment
#> [1] "SummarizedExperiment" "GenomicRanges"        "BiocBaseUtils"       
#> [4] "BiocGenerics"         "DelayedArray"         "S4Vectors"           
#> [7] "IRanges"              "Biobase"             
#> 

pkgBiocDeps("MultiAssayExperiment", only.bioc = FALSE)
#> $MultiAssayExperiment
#>  [1] "SummarizedExperiment" "methods"              "GenomicRanges"       
#>  [4] "BiocBaseUtils"        "BiocGenerics"         "DelayedArray"        
#>  [7] "S4Vectors"            "IRanges"              "Biobase"             
#> [10] "stats"                "tidyr"                "utils"               
#>