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 STexampleData and 10xVisiumData packages, and how to generate plots with the ggspavis package.

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

Link

https://drighelli.github.io/SpatialExperiment_Bioc2021/index.html

Authors

• Dario Righelli (dario.righelli@gmail.com)
• Helena L. Crowell (helena.crowell@uzh.ch)
• Lukas M. Weber (lukas.weber@jhu.edu)

Pre-requisites

• Basic R syntax knowledge and R data structures
• Familiarity with SingleCellExperiment and/or SummarizedExperiment classes

Available resources

• Link to the pkgdown website.
• Link to Docker image.
• The SpatialExperiment package link.
• The STexampleData package link.
• The TENxVisiumData package link.
• The ggspavis package link.

To use the Docker image

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 abc.