## First, install the BiocManager package, which will allow you to install packages from Bioconductor install.packages("BiocManager") ## Next, install Bioconductor BiocManager::install() ## or check that you have a valid installation BiocManager::valid() ## Then, run the following code to install the necessary packages. This can take some time. pkg <- c("AnnotationDbi", "DESeq2", "DT", "ReportingTools", "SummarizedExperiment", "apeglm", "fgsea", "genefilter", "ggbeeswarm", "macrophage", "org.Hs.eg.db", "pheatmap", "reactome.db", "tidyverse", "tximeta") BiocManager::install(pkg) ## Finally, check that you can load the packages, i.e., that the following runs without errors suppressPackageStartupMessages({ invisible(lapply(pkg, library, character.only = TRUE)) }) ## To save some time in the lecture, prepare/download reference annotation dir <- system.file("extdata", package = "macrophage") se <- tximeta(coldata = data.frame(names = "SAMEA103885102", files = file.path(dir, "quants", "SAMEA103885102", "quant.sf.gz"), stringsAsFactors = FALSE), type = "salmon", dropInfReps = TRUE) ## For more information and troubleshooting, visit https://www.bioconductor.org/install/ library(BiocStyle)