Introduction to eQTL analysis

This repository contains the materials for an introductory eQTL analysis course.

Docker image

The docker directory contains the Dockerfile and data necessary to build a Docker image that contains all necessary components for the exercises that form part of this course. The resulting Docker image is available from DockerHub. docker pull humburg/eqtl-intro will pull the latest version of the image.

Installing Docker

Using this image requires a working Docker installation. Installation instructions for Windows, Mac, Ubuntu and a number of other platforms are available through the Docker documentation.

Using the Docker image

The docker image contains R and RStudio server and allows use of the RStudio IDE as well as the R console. To use the IDE start the Docker container with

docker run -p 8787:8787 humburg/eqtl-intro

RStudio is then available through your web browser by accessing the docker host on port 8787. On Linux the docker host is 127.0.0.1 (or localhost) by default. So the full URL to RStudio is http://localhost:8787. On Mac or Windows, running boot2docker, you can determine the docker host with the boot2docker ip command. Log in to RStudio with the username rstudio and password rstudio.

To successfully complete the exercises it is necessary to share files with the local machine. Instructions on how to do this on Windows, Mac and Linux are available here.