Install R and Rstudio

Install [R version 4.1 or higher] (https://cran.r-project.org/)
Install Rstudio

Install msqrob2

Install msqrob2, start R and run the following command.

if(!requireNamespace("BiocManager", quietly = TRUE)) {
 install.packages("BiocManager")
}
BiocManager::install("msqrob2")

Participants who want to use the graphical user interface (GUI) can install the msqrob2gui shiny app, start R and run the following commands

if(!requireNamespace("BiocManager", quietly = TRUE)) {
 install.packages("BiocManager")
}
if(!requireNamespace("remotes", quietly = TRUE)) {
 BiocManager::install("remotes")
}
BiocManager::install("statomics/msqrob2gui")

check if your installation is working with the following example

library(msqrob2)
data(pe)
pe <- aggregateFeatures(pe,i="peptide",fcol="Proteins",name="protein")
pe <- msqrob(pe,i="protein",formula=~condition,modelColumnName="rlm")
getCoef(rowData(pe[["protein"]])$rlm[[1]])

Install TargetDecoy for QC of decoys

Install TargetDecoy, start R and run the following command.

if(!requireNamespace("BiocManager", quietly = TRUE)) {
 install.packages("BiocManager")
}
if(!requireNamespace("remotes", quietly = TRUE)) {
 BiocManager::install("remotes")
}
BiocManager::install("statomics/TargetDecoy")

Check if your installation is working with the following example

library(TargetDecoy)
data("ModSwiss")
evalTargetDecoys(ModSwiss,"isdecoy","ms-gf:evalue")