This three-parts workshop provides basics backgroud and the instruments to start to work with spatial transcriptomics with R/Bioconductor.

The first part is an overview of the most widely used technologies for spatially resolved transcriptomics, such as seqFISH and 10x Genomics Visium, and the main differences between them.

The second part is mainly focused on the SpatialExperiment class and how to handle its methods for storing and retrieving spatial coordinates, images, and how to manage them.

The third part will show how to store/retrieve already stored spatial datasets from the STdata package and how to generate plots with ggspavis.

The workshop will end with a mini-challenge for the attendees to handle with provided tools during the sessions.


Available Resources

  • Link to the pkgdown website.
  • Link to Docker image.
  • The SpatialExperiment (under development) class used in this workshop at github.
  • The STdata package link.
  • The ggspavis package link.

To use the Docker image:

We highly suggest to use the docker image within all the needed material.

docker run -e PASSWORD=<SET_A_PASSWORD> -p 8787:8787 drighelli/eurobioc2020spatialworkshop

Once running, navigate to https://localhost:8787/ and then login with rstudio:<YourChosenPassword>.