We will work with R and Rmarkdown. Also consider installing RStudio.
You can use this script to install packages from both CRAN and BioConductor. Kindly install the software in advance.
.bioc_packages <- c("ade4", "dada2", "DECIPHER", "dplyr", "genefilter", "ggplot2", "ggrepel", "ggtree", "impute", "microbiome", "phangorn", "philr", "phyloseq", "PMA", "tidyverse", "vegan")
.cran_packages <- c("adaptiveGPCA", "ade4", "caret", "devtools", "dplyr", "e1071", "earlywarnings", "ggnetwork", "ggplot2", "ggrepel", "gridExtra", "igraph", "intergraph", "knitr", "miniUI", "nlme", "phyloseq", "phyloseqGraphTest", "pls", "plyr", "PMA", "randomForest", "reshape2", "rmarkdown", "scales", "shiny", "structSSI", "vegan")
.github_packages <- c("jfukuyama/phyloseqGraphTest", "PratheepaJ/bootLong", "Hallucigenia-sparsa/seqtime")
# Install CRAN packages (if not already installed)
.inst <- .cran_packages %in% installed.packages()
if (any(!.inst)){
install.packages(.cran_packages[!.inst],repos = "http://cran.rstudio.com/")
}
.inst <- .github_packages %in% installed.packages()
if (any(!.inst)){
devtools::install_github(.github_packages[!.inst])
}
.inst <- .bioc_packages %in% installed.packages()
if(any(!.inst)){
BiocManager::install(.bioc_packages[!.inst])
}