Install Packages Script

# R Packages needed for the 2025 Omics Workshop Day 2

# if asked to update: n     DO NOT DO IT --- JUST SAY NO. If you get an error then we can fix it
# if asked if you want to install from source: Yes
# if asked to install additional tools say yes!


# CRAN
install.packages("here")
install.packages("pheatmap")
install.packages("dplyr")
install.packages("ggplot2")
install.packages("patchwork")
install.packages("dplyr")
install.packages("tibble")
install.packages("tidyr")
install.packages("devtools")
install.packages("remotes")
install.packages("Seurat")


# Bioconductor # R 4.5 or newer

install.packages("BiocManager")
BiocManager::install("SingleR")
BiocManager::install("scater")
BiocManager::install("scDblFinder")
BiocManager::install("clusterProfiler") # needs fgsea
BiocManager::install("pathview")
BiocManager::install("enrichplot")
BiocManager::install("decoupleR")


# github install
remotes::install_github('satijalab/seurat-wrappers')
devtools::install_github("digitalcytometry/cytotrace2", subdir = "cytotrace2_r")



# needs tools install
devtools::install_github("immunogenomics/presto") # requires software installation for mac, optional package
devtools::install_github("jinworks/CellChat") # requries tools installation for mac


# codependencies for monocle3
BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
                       'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment',
                       'SummarizedExperiment', 'batchelor', 'HDF5Array',
                       'ggrastr'))

remotes::install_github("bnprks/BPCells/r")
devtools::install_github('cole-trapnell-lab/monocle3')


# Check install
library(here)
library(pheatmap)
library(dplyr)
library(ggplot2)
library(patchwork)
library(dplyr)
library(tibble)
library(tidyr)
library(devtools)
library(remotes)
library(Seurat)
library(SingleR)
library(scater)
library(scDblFinder)
library(clusterProfiler)
library(pathview)
library(enrichplot)
library(decoupleR)
library(SeuratWrappers)
library(presto)
library(CellChat)
library(CytoTRACE2)
library(monocle3)