Instructor: John Lawson, University of Virginia (firstname.lastname@example.org)
This workshop will detail how to annotate inter-sample epigenetic variation with publicly available gene regulatory information, for example, associating epigenetic variation with transcription factor-binding regions. We will spend a few minutes at the beginning introducing the goals of the package and important concepts. Then, we will go through several simplified example applications from the COCOA vignette. We will cover both unsupervised and supervised analyses. Finally, we will finish with some best practices for covariation-based analyses.
We will work through the COCOA vignette. The vignette and results will be displayed for participants but they may also go through the vignette on their computers.
docker run -e PASSWORD=yourpassword -p 8787:8787 -d —rm databio/cocoa_workshop_bioc2020. Use
-v $(pwd):/home/rstudioargument to map your local directory to the container.
yourpassword. Note that on Windows you need to provide your localhost IP address like
http://18.104.22.168:8787/- find it using
docker-machine ip defaultin Docker’s terminal.
browseVignettes(package = "COCOA.workshop.BIOC2020"). Click on one of the links, “HTML”, “source”, “R code”.
The requested page was not founderror, add
help/to the URL right after the hostname, e.g., http://localhost:8787/help/library/COCOA.workshop.BIOC2020/doc/IntroToCOCOA.html. This is a known bug.