Hi,
I work with the version 4.1.3 and I used tis scripts:
.cran_packages <- c("tidyverse", "cowplot", "picante", "vegan", "HMP", "dendextend", "rms", "devtools")
.bioc_packages <- c("phyloseq", "DESeq2", "microbiome", "metagenomeSeq", "ALDEx2")
.inst <- .cran_packages %in% installed.packages()
if(any(!.inst)) {
install.packages(.cran_packages[!.inst])
}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(.bioc_packages, version = "3.14")
devtools::install_github("adw96/breakaway")
devtools::install_github(repo = "malucalle/selbal")
library(DESeq2)