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Install R/Rstudio

You can install R from the CRAN repository. Yo will need R version 4.5 or higher.

You can install from the Posit website.

Install the GitHub and Bioconductor installers

Open Rstudio and paste the following command in the console:

install.packages("devtools")
install.packages("BiocManager")
BiocManager::install(version = "devel")

The first command will install a utility package that will enable to install packages from GitHub. The second line will install the Bioconductor package installer. Ensure the installation succeeded by running the following command:

BiocManager::version()
## [1] '3.19'

It should return 3.22 or higher.

Install QFeatures

The workshop will require a specific version of QFeatures, you can install it using the following command:

BiocManager::install("cvanderaa/QFeatures", ref = "uniquePrecId")

Test the package has been correctly installed using the following command:

library(QFeatures)
data(feat2)
joinAssays(feat2, 1:3, fcol = "Prot")
## An instance of class QFeatures (type: bulk) with 4 sets:
## 
##  [1] assay1: SummarizedExperiment with 10 rows and 4 columns 
##  [2] assay2: SummarizedExperiment with 4 rows and 4 columns 
##  [3] assay3: SummarizedExperiment with 7 rows and 4 columns 
##  [4] joinedAssay: SummarizedExperiment with 14 rows and 12 columns

Install msqrob2

The workshop will also require a specific version of msqrob2, you can install it using the following command:

BiocManager::install("statOmics/msqrob2") ## this installs msqrob2

Test whether the package has been correctly installed using the following command:

library(msqrob2)
data(pe)
pe <- aggregateFeatures(
    pe, i = "peptide", fcol = "Proteins", name = "protein"
)
msqrob(pe,i = "protein", formula = ~ condition)
## An instance of class QFeatures (type: bulk) with 2 sets:
## 
##  [1] peptide: SummarizedExperiment with 631 rows and 20 columns 
##  [2] protein: SummarizedExperiment with 100 rows and 20 columns

Install the graphical user interfaces

In this course, we will use 2 graphical user interfaces (GUIs): QFeaturesGUI for the data preprocessing and msqrob2gui for the data modelling. For installing the GUIs, you’ll again need to install specific versions as the software is still in a developmental stage.

BiocManager::install("statOmics/QFeaturesGUI") ## this installs QFeaturesGUI
BiocManager::install("statOmics/msqrob2gui", ref = "gui2modules") ## this installs msqrob2gui

Test whether the QFeaturesGUI package has been correctly installed using the following command:

QFeaturesGUI::importQFeatures()

This should open a new window. You can close it for now.

Test whether the msqrob2gui package has been correctly installed using the following command:

msqrob2gui::launchMsqrob2App()

Again, this should open a new window, but you can close it for now.