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Short Description
RStudio with QTL mapping packages (DOQTL, qtl2, intermediate)
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Short Course on Systems Genetics 2016

This is a repository for Short Course on Systems Genetics (October 16 - 21, 2016) at The Jackson Laboratory that includes the following tutorials:

  • DOQTL (D Gatti) [markdown]: kinship matrix, linkage and association mapping, eQTL viewer
  • DESeq2 (P Simecek) [markdown]: detect differential expression between groups of RNASeq samples
  • Mediation analysis (S Munger & P Simecek) [markdown]: find an intermediate between genotype and trans-regulated gene/protein
  • How to start Digital Ocean droplet? [markdown] How to run the customized RStudio in the cloud
    The participants use their web browsers to connect to customized Docker containers hosted on Digital Ocean virtual machines (see screen captures below).

Docker is a lightweight container virtualization platform. We created three Docker images for this course: churchill/doqtl (RStudio, DOQTL, DESeq2), churchill/asesuite (kallisto, EMASE) and churchill/webapp (eQTL/pQTL viewer). You can run docker containers on your computer or in the cloud environments like AWS, Digital Ocean, Microsoft Azure or Google Cloud. Dockerfiles can also serve as a list of instructions how to install the software on your computer. See here how to set up your own RStudio in the cloud.

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