This workshop gives an introductory overview of the DelayedArray framework, which can be used by R / Bioconductor packages to support the analysis of large array-like datasets. A DelayedArray is like an ordinary array in R, but allows for the data to be in-memory, on-disk in a file, or even hosted on a remote server.
Workshop participants will learn where they might encounter a DelayedArray in the wild while using Bioconductor and understand the fundamental concepts underlying the DelayedArray framework. This workshop will feature introductory material, ‘live’ coding, and Q&A, all of which are adapted from the content below.
Students will be able to run code examples from the workshop material. There will be a Q&A session in the second half of the workshop.
These packages are the focus of this workshop:
Please see the workshop
DESCRIPTION for a full list of dependencies.
|Introductory material||8 min|
|First contact||30 min|
|Workflow tips for DelayedArray-backed analyses||5 min|
This workshop uses Bioconductor version 3.12. At the time of writing, this is the current ‘devel’ version of Bioconductor, which can be installed following these instructions.
You can then install the packages necessary for this workshop using the following:
Alternatively, you can might like to use Docker to runt he workshop in a container with R, all the necessary packages, and RStudio. This can be done as follows:
docker run -e PASSWORD=delayedarray -p 8787:8787 -d --rm petehaitch/bioc2020_delayedarray_workshop. 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://126.96.36.199:8787/- find it using
docker-machine ip defaultin Docker’s terminal.
browseVignettes(package = "DelayedArrayWorkshop"). 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/DelayedArrayWorkshop/doc/Effectively_using_the_DelayedArray_framework_for_users.html. This is a known bug.