| # check if R is installed | |
| which R > /dev/null | |
| if [[ $? -ne 0 ]]; then | |
| echo "R is not installed!" | |
| exit 1 | |
| fi | |
| which Rscript > /dev/null | |
| if [[ $? -ne 0 ]]; then | |
| echo "Rscript is not installed!" | |
| exit 1 | |
| fi | |
| Rscript -e ' | |
| install.packages( | |
| c( | |
| "dplyr", | |
| "ggbreak", | |
| "ggplot2", | |
| "ggthemes", | |
| "jsonlite", | |
| "kableExtra", | |
| "knitr", | |
| "openxlsx", | |
| "optparse", | |
| "patchwork", | |
| "plotly", | |
| "plyr", | |
| "pracma", | |
| "RColorBrewer", | |
| "readr", | |
| "safetensors", | |
| "stringr", | |
| "this.path", | |
| "tidyverse" | |
| ) | |
| ) | |
| if (!require("BiocManager", quietly = TRUE)) | |
| install.packages("BiocManager") | |
| BiocManager::install("ComplexHeatmap") | |
| install.packages( | |
| "ggmagnify", | |
| repos = c( | |
| "https://hughjonesd.r-universe.dev", | |
| "https://cloud.r-project.org" | |
| ) | |
| ) | |
| ' | |