Installation

Installing using python

To use SPOT (python version), first install its dependencies using pip or conda.

Attention

To run SPOT with cluster dependent modules, you must specify cluster fields. One recommended spatial clustering method is Cellcharter [1].

Alternatively, we provide a Non-negative Matrix Factorization (NMF) model for simple analysis.

You can simply install SPOT dependencies using pip through:

(.venv) $ pip install numpy pandas scipy scikit-learn anndata scanpy

SPOT can be ran on both Linux and Mac OS, since it is interpreted by python and R.

Note

Both python and R version requires python to run Cluster dependent analysis. since they require Cellcharter to perform clustering.

If other clustering method is performed, follow the instructions in Build your first project to perform downstream analysis.

Installing using R

To install SPOT (R version), first intall dev-tools

$ install.packages('devtools')
$ devtools::install_github("pkuTrasond/SPOT")

R will automatically install all the dependencies.

Note

R version 4.2.2 is reconmended.

[1]

Varrone, M., Tavernari, D., Santamaria-Martínez, A. et al. CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity. Nat Genet 56, 74–84 (2024).