Workshop resources

On this page, we’ve assembled some resources you may find helpful during your own data journey as well as during consultation sessions during the workshop. For more information about the structure of consultation sessions and how to get help, please review the Consultation sessions section of the Workshop Structure page.

Table of contents

• Module cheatsheets
• Working with your own data on RStudio Server
• Working on your own computer
• Topic-specific resources
  • R programming
  • Bulk transcriptomics data
  • Single-cell RNA-seq data

Module cheatsheets

The modules-cheatsheets directory of our GitHub repository of training materials contains Markdown and PDF version of “cheatsheets” that contain tables with short descriptions of functions used throughout training modules and links to documentation.

• Introduction to R/Tidyverse cheatsheet (View Markdown, Download PDF)
• Bulk RNA-seq module cheatsheet (View Markdown, Download PDF)
• Introduction to single-cell RNA-seq module cheatsheet (View Markdown, Download PDF)
• Advanced to single-cell RNA-seq module cheatsheet (View Markdown, Download PDF)
• Converting among single-cell data formats cheatsheet (View Markdown, Download PDF)

You may find these helpful as you review instruction material or work through exercise notebooks.

Working with your own data on RStudio Server

If you plan on working with your own data during consultations, you may find it helpful to leverage our RStudio Server.

You can find instructions for working with your own data on RStudio Server here. Please read these instructions carefully.

We’ll reiterate some of the most important points from those instructions below:

• As a rule of thumb, if the data you are working with would be released under controlled access, rather than made publicly available, at the time of publication of a scientific manuscript, it should not be uploaded to our RStudio Server.
• You have 50GB of space available. If your data is larger than 50GB, please contact an instructor.

Working on your own computer

After your access to the RStudio Server has ended, you may wish to continue working in a computing environment that matches what we used during the workshop. Follow these instructions for how you can set up a local environment on your own computer that reproduces, to the extent possible, the workshop computing environment.

Topic-specific resources

R programming

See this page for recommendations on getting started with R programming, as well as some links to useful external resources on R.

Bulk transcriptomics data

See this page for more resources on working with bulk transcriptomics data, including RNA-seq and microarray. Resources include how to find practice datasets to work with as well as information about transcriptome indices we have built for processing raw bulk RNA-seq data.

Single-cell RNA-seq data

See this page for more resources on working with scRNA-seq.

Resources include how to find practice datasets to work with as well as a list of external resources for performing common analyses in scRNA-seq data.