Standardizing workflows in imaging transcriptomics with the abagen toolbox

Overview of this walkthrough

This walkthrough is designed to accompany the manuscript “Standardizing workflows in imaging transcriptomics with the abagen toolbox” by RD Markello and colleagues. While we strove to be detailed in our manuscript, we acknowledge that working through code and data files (however well-documented) to reproduce results from other people can be…frustrating. This walkthrough attempts to lay out the relevant steps required to install + set up your computing environment, how to get access to the (minimal) data required to run the code, and what commands + scripts you need to run to re-generate our results. Of course, you’ll need to refer to the actual code files in our GitHub repository for this to all make sense, but hopefully it helps make this whole reproducibility process a bit less garish.

Note that the vast majority of the code that was used in the analyses resides in the abagen toolbox; this repository really just contains the wrapper code we used to call abagen!

Questions?

If anything in this walkthrough (or in our repository or our manuscript!) is confusing / unclear / whathaveyou, you can reach out by either (1) opening an issue on our GitHub repository, or (2) emailing Ross.