installNetCoMiPacks: Install all packages used within NetCoMi

In stefpeschel/NetCoMi: Network Construction and Comparison for Microbiome Data

Install all packages used within NetCoMi

Description

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.

stefpeschel/NetCoMi documentation built on Feb. 4, 2024, 8:20 a.m.