Repository of spatial datasets analyzed by Giotto. Each dataset has its own folder with subfolders for:
- count matrix
- locations
- giotto R-script with secondary analyis (when available)
- raw data (optional)
These datasets can be downloaded directly from within the Giotto package using the function getSpatialDataset as illustrated in the examples.
Visium datasets are not available, but the original directory can be downloaded from the 10X Visium website and directly used as input for the wrapper createGiottoVisiumObject to create a Giotto object.
Small crops of public Xenium, Stereo-seq, CosMx and Visium HD runs, in each
vendor's own output layout, for testing readers and pipelines. They are release
assets, downloaded with GiottoData::getSpatialDataset(); the scripts that
made them are in crops/.
- website
- slide-seq
- MIBI
- ...