On this page, we’ve assembled some resources you may find helpful for working with spatial transcriptomic data. Please note, spatial transcriptomics is an emerging field, and new methods and packages are rapidly being developed! Resources on this page are not comprehensive.

Table of contents

Obtaining practice datasets

The Single-Cell Pediatric Cancer Atlas (ScPCA)

The Childhood Cancer Data Lab builds and maintains the Single-cell Pediatric Cancer Atlas (ScPCA) Portal, a resource of single-cell/nuclei transcriptomic data generated by ALSF-funded labs and uniformly processed by the Data Lab. Some of these projects contains spatial transcriptomic data, available as raw Space Ranger output files. You can read more about how we process data in ScPCA and how you can use ScPCA datasets in our documentation.

10x Genomics

The 10x Genomics website has a datasets page where you can search for and download spatial transcriptomics data

Additional spatial transcriptomics resources

This list provides some links to external resources on spatial transcriptomics analysis methods that may be useful to you as you develop your own analysis skills and practices.