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I was wondering if there is more elegant way of installing and loading multiple packages in Bioconductor similar to pacman with CRAN packages.

I tried:


# install and load  the package  manager
 if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# install and load bioconductor packages 
bio_pkgs = c("BiocManager", "ggbio", "biomaRt", "EnsDb.Hsapiens.v75", "cBioPortalData", "GenomicRanges", "GenomicFeatures", "TxDb.Hsapiens.UCSC.hg19.knownGene", "Homo.sapiens")

 if (!requireNamespace(bio_pkgs, quietly = TRUE))
    BiocManager::install(bio_pkgs)

library(easypackages)
libraries("ggbio", "biomaRt", "EnsDb.Hsapiens.v75", "renvcBioPortalData", "GenomicRanges", "GenomicFeatures", "TxDb.Hsapiens.UCSC.hg19.knownGene", "Homo.sapiens")

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You can do something like this:

bio_pkgs <- c("ggbio", "biomaRt", "EnsDb.Hsapiens.v75", "renvcBioPortalData", 
          "GenomicRanges", "GenomicFeatures", "TxDb.Hsapiens.UCSC.hg19.knownGene", "Homo.sapiens")

# install:
BiocManager::install(bio_pkgs)

# load all at once
invisible(lapply(pkgs, function(x) library(x, character.only=TRUE)))

Be aware though that if you version-control your packages with something like renv then it is encouraged to explicitely load every package as suggested here so renv can properly recognize the packages to snapshot.

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  • $\begingroup$ Thank you ATpoint, this is way more elegant :) $\endgroup$
    – Sam
    Jan 25 '21 at 12:20

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