This three-part workshop provides background and tools to start working with spatially resolved transcriptomics data with R/Bioconductor.
The first part is an overview of the most widely used technologies for spatially resolved transcriptomics, such as 10x Genomics Visium and seqFISH, and the main differences between them.
The second part is 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 retrieve datasets in
SpatialExperiment format from the
10xVisiumData packages, and how to generate plots with the
The workshop will end with a mini-challenge for attendees using the tools provided during the sessions.
We recommend using the Docker image, which contains all required material. Note this is a large download (~1.5 GB).
docker run -e PASSWORD=abc -p 8787:8787 drighelli/spatialexperiment_bioc2021:latest
Once running, navigate to http://localhost:8787/ and then login with username
rstudio and password