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.
https://drighelli.github.io/SpatialExperiment_Bioc2021/index.html
- Dario Righelli (dario.righelli@gmail.com)
- Helena L. Crowell (helena.crowell@uzh.ch)
- Lukas M. Weber (lukas.weber@jhu.edu)
- Basic R syntax knowledge and R data structures
- Familiarity with SingleCellExperiment and/or SummarizedExperiment classes
- 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.
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
.