01-reqs.Rmd

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# Technical requirements

## R-based

[R](https://www.r-project.org/) is one of the most popular programming languages for Bioinformatics. We aimed to only use R packages in this course. However, a few tools that we describe ([SNN-Cliq](http://bioinfo.uncc.edu/SNNCliq/) and [MAGIC](https://github.com/pkathail/magic)) are Python-based.

## Docker image (RStudio)

The course can be reproduced without any package installation by running the course docker RStudio image which contains all the required packages.

Make sure Docker is installed on your system. If not, please follow [these instructions](https://docs.docker.com/engine/installation/). To run the course RStudio docker image:

```
docker run -d -p 8787:8787 quay.io/hemberg-group/scrna-seq-course-rstudio
```

This download the docker image (may take some time) and start a new Rstudio session in a docker container with all packages installed and all data files available.

Then visit `localhost:8787` in your browser and log in with `username:password` as `rstudio:rstudio`. Now you are ready to go!

## Manual installation

If you are not using a docker image of the course, then to be able to run all code chunks of the course you need to clone or download the [course GitHub repository](https://github.com/hemberg-lab/scRNA.seq.course) and start an R session in the cloned folder. You will also need to install all packages listed in the course [Dockerfile](https://github.com/hemberg-lab/scRNA.seq.course/blob/master/Dockerfile).

Alternatively, you can just install packages listed in a chapter of interest.