An introductory course
This website contains the materials for an introductory eQTL analysis course. The main focus is on the use of linear models for the detection of associations between SNPs and gene expression.
The material contains several exercises that use R for various data manipulation and analysis tasks. Basic familiarity with this language will therefore be helpful.
The slides for the course are available here. A number of related exercises and suggested solution are also available.
A docker image containing all software required to carry out the exercises as well as most of the required data is available from DockerHub.