---
# System prepended metadata

title: FlowCytoWorkshop_installation
tags: [Book, Templates]

---

# Workshop for Analysis of Full Spectrum Flow Cytometry Data using R <i class="fa fa-book fa-fw"></i>

[![hackmd-github-sync-badge](https://hackmd.io/lsA-178cTGe8Cac-hbqq1g/badge)](https://hackmd.io/lsA-178cTGe8Cac-hbqq1g)


## Installations instructions
Welcome to the **Workshop for Analysis of Full Spectrum Flow Cytometry Data using R**! :fireworks: Before the start of the workshop, you will need to make sure all the required packages are installed and available. 

### Pre-requisites
For the following instructions, we assume you have already installed and updated **R**, **Rstudio**, and **FlowJo** on your computer. If this is not the case, please visit the [Rstudio](https://posit.co/download/rstudio-desktop/) or [FlowJo](https://www.flowjo.com/solutions/flowjo/downloads) site and follow the installation instructions for your operating system.

### Step 1 - Download/clone github repository
---
- **Step 1.1:** Go to https://github.com/RTCure/CytometryWorkshop. 

- **Step 1.2:** If you already have a github account, you can clone the repository, otherwise download the whole repository as a zip file. 

![Screenshot 2024-01-16 at 10.39.13](https://hackmd.io/_uploads/Skbe-eVY6.png)

![download_githubrepo-ezgif.com-optimize](https://hackmd.io/_uploads/Hk5I1gEKa.gif)



- **Step 1.3:** If you chose to downloaded the zip file, go to your `downloads` folder, locate the file `CytometryWorkshop-master.zip` and double click on it to unzip it. We advise you to move the directory to another location of your preference so it doesn't get lost in your `downloads` directory. If you chose to clone the repository, make sure the `CytometryWorkshop` directory is present in the folder you cloned it into.

### Step 2 - Open R studio
---
Once you have downloaded/cloned the CytometryWorkshop repository, open a new Rstudio window.

- **Step 2.1:** On the Rstudio window, go to the top bar and select **file > open project**.

![Screenshot 2024-01-16 at 11.02.30](https://hackmd.io/_uploads/SkieSCXF6.png)

- **Step 2.2:** Select the location of the `CytometryWorkshop-master` folder and click `open`.

- **Step 2.3:** Once the project is loaded, enter the following commands on the r console.
```r
renv::activate()
```
This command should run without errors. 
```r
renv::restore()
```
If you get the message `- Unrecognized response: please enter 'y' or 'n', or type Ctrl + C to cancel`, choose 'y' and click enter. It is possible that this command only installs BiocManager initially. If you get the message `Successfully installed 1 package in x.x seconds` you will need to re-run the `renv::restore()` command.

This will take some minutes (sit down and relax :popcorn::doughnut::coffee:), and it should run without errors. At the end of the process you should have all the packages needed for the course :tada:. 


:::danger
***Please do not edit anything above this line***
:::



## Questions?
If you have encountered any problems or have any questions, feel free drop a question below:
:::info
:::spoiler Q&A
1. Please provide deatails about your Operating System (OS), R and Rstudio version you're using, and Error log.
2. Your question will go here... :+1: 
3. 
4. 
5. 
6. 
:::



###### tags: `FlowCytometry` `Workshop`
