Datasets: Visium additional tissues

Lukas M. Weber

Leader(s)

Difficulty & duration

  • difficulty: intermediate
  • duration: 1-2 days

Abstract

Our current aims are:

  • Finalize SpatialExperiment class structure by creating and testing example datasets from several technological platforms (to be collected in STdata package)
  • Adapt visualization functions for data from each platform (to be collected in ggspavis package)
  • Create a short analysis workflow using one of the example datasets from each platform

This will allow us to build an integrated Bioconductor-based infrastructure for analyzing spatially resolved transcriptomics data. Ultimately, this will all be showcased in our OSTA online book.

So far, we have mainly worked with data from the 10x Genomics Visium platform. The STdata package (under development) currently contains two example datasets from the Visium platform (human DLPFC and mouse coronal).

In this set of “Dataset” challenges, we will aim to select and prepare several additional datasets for demonstration and testing purposes.

Our existing Visium datasets are from brain tissue (mouse and human). However, datasets from other tissues are also available from the 10x Genomics website. These could be used for additional examples, and would be more easily accessible for users if we make them available as SpatialExperiment objects.

Targets

This challenge consists of:

  • choosing one or more of the additional Visium datasets from the 10x Genomics website (e.g. from different tissues)
  • formatting them into SpatialExperiment objects
  • creating reproducible scripts to create the objects from the raw data files, saving the objects, and adding these to the STdata package

As a starting point, we can use the make-data.R scripts from the existing objects in the STdata package: