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Install all packages used within NetCoMi

Source: R/installNetCoMiPacks.R
installNetCoMiPacks.Rd

This function installs the R packages used in NetCoMi not listed as dependencies or imports in NetCoMi's description file. These are optional packages only needed in certain network construction settings.

BiocManager::install is used for installation since it installs or updates Bioconductor as well as CRAN packages.

Installed CRAN packages:

  • cccd

  • LaplacesDemon

  • propr

  • zCompositions

Installed Bioconductor packages:

  • ccrepe

  • DESeq2

  • discordant

  • limma

  • metagenomeSeq

If not installed via this function, the packages are installed by the respective NetCoMi functions when needed.

Usage

installNetCoMiPacks(onlyMissing = TRUE, lib = NULL, ...)

Arguments

onlyMissing

logical. If TRUE (default), installed.packages is used to read out the packages installed in the given library and only missing packages are installed. If FALSE, all packages are installed or updated (if already installed).

lib

character vector giving the library directories where to install missing packages. If NULL, the first element of .libPaths is used.

...

Additional arguments used by install or install.packages.