This workshop demonstrates the use of the iSEE package to create and configure interactive applications for the exploration of various types of genomics data sets (e.g., bulk and single-cell RNA-seq, CyTOF, gene expression microarray).
This workshop will be presented as a lab session that combines an instructor-led live demo, followed by hands-on experimentation guided by completely worked examples and stand-alone notes that participants may continue to use after the workshop.
The instructor-led live demo comprises three parts:
The hands-on lab comprises three parts:
Participants are encouraged to ask questions at any time during the workshop.
Additional background reading about the programming environment, relevant packages, and example use cases:
Students will participate by following along an R markdown document, and asking questions throughout the workshop. There is also scope for participants to apply iSEE to their own data sets, and fuel the discussion with more questions about specific use cases.
SingleCellExperimentfor downstream analyses and visualization
In the Docker settings menu:
docker pull iseedevelopers/iseeworkshop2020
docker run -e PASSWORD=isee -p 8787:8787 -d --rm iseedevelopers/iseeworkshop2020. Use
-v $(pwd):/home/rstudioargument to map your local directory to the container.
isee. Note that on Windows you need to provide your localhost IP address like
http://220.127.116.11:8787/- find it using
docker-machine ip defaultin Docker’s terminal.
browseVignettes(package = "iSEEWorkshop2020"). 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/iSEEWorkshop2020/doc/iSEE-lab.html. This is a known bug.