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
The workshop will end with a mini-challenge for the attendees to handle with provided tools during the sessions.
SpatialExperiment(under development) class used in this workshop at github.
We highly suggest to use the docker image within all the needed material.
Once running, navigate to https://localhost:8787/ and then login with