PDA25EBI/software.Rmd at master · statOmics/PDA25EBI · GitHub

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---
title: Software for Proteomics Data Analysis (PDA)
author: "Lieven Clement"
date: "[statOmics](https://statomics.github.io), Ghent University"
output:
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---

<a rel="license" href="https://creativecommons.org/licenses/by-nc-sa/4.0"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png" /></a>

## Install R/Rstudio

You can install R from the [CRAN repository](https://cran.r-project.org/).
Yo will need R version 4.5 or higher.

You can install from the [Posit website](https://posit.co/download/rstudio-desktop/).

## Install the GitHub and Bioconductor installers

Open Rstudio and paste the following command in the console:

```{r, eval=FALSE}
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:

```{r, warning=FALSE, message=FALSE}
BiocManager::version()
```

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:

```{r, eval=FALSE}
BiocManager::install("cvanderaa/QFeatures", ref = "uniquePrecId")
```

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

```{r, warning=FALSE, message=FALSE}
library(QFeatures)
data(feat2)
joinAssays(feat2, 1:3, fcol = "Prot")
```

## Install msqrob2

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

```{r, eval=FALSE}
BiocManager::install("statOmics/msqrob2") ## this installs msqrob2
```

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

```{r, warning=FALSE, message=FALSE}
library(msqrob2)
data(pe)
pe <- aggregateFeatures(
    pe, i = "peptide", fcol = "Proteins", name = "protein"
)
msqrob(pe,i = "protein", formula = ~ condition)
```
## 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.

Note, that [QFeaturesGUI](https://github.com/UCLouvain-CBIO/QFeaturesGUI) is actively developed and maintained by the Laurent Gatto lab.
However, we forked QFeaturesGUI temporarily for this version of the course because we needed some additional functionalities.

```{r, eval=FALSE}
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:

```{r, eval=FALSE}
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:

```{r, eval=FALSE}
msqrob2gui::launchMsqrob2App()
```

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