spatial datasets
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.
Available datasets
2022
Molecular Cartography Human Lung
single-cell Human Prostate
single-cell Mouse Brain
2020
Spatial Transcriptomics squamous cell carcinoma
2019
Visium kidney
Visium brain
merFISH
seqFISH+ somatosensory cortex
seqFISH+ olfactory bulb
slide-seq cerebellum
2018
STARmap 3D cortex
osmFISH somatosensory cortex
merFISH 3D hypothalamic preoptic region
CODEX spleen
CyCIF PDAC
MIBI TNBC
2016
Spatial Transcriptomics olfactory bulb
Soon available datasets
- slide-seq
- MIBI
- ...