SpatialDE

Helena L. Crowell

University of Zurich

Leader(s)

Difficulty & duration

  • intermediate to advanced
  • less than a week

Abstract

SpatialDE by Svensson et al. 2018 is a method to identify spatially variable genes (SVGs) in spatially resolved transcriptomics data.

We have previously used this method in our paper Maynard and Collado-Torres et al. 2020.

SpatialDE is available as a Python package (see https://github.com/Teichlab/SpatialDE), which makes it difficult to integrate into R/Bioconductor-based workflows. In this challenge, our aim is to make SpatialDE accessible in R using either reticulate or basilisk.

Targets

  • create a wrapper for SpatialDE in R, using either basilisk or reticulate (basilisk is preferred, although the choice of which tool to use will depend on interest and experience)
  • write a short script (e.g. in RMarkdown) with an example workflow showing how to use the wrapper

If this is successful, we can integrate this into our example workflows, e.g. in our OSTA online book currently under development.