cell2location jupyter python interface

BayraktarLab/cell2location: Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model) (github.com) 

conda create -y -n cell2loc_env python=3.9

conda activate cell2loc_env
pip install cell2location -i douban.com
Finally, to use this environment in jupyter notebook, add jupyter kernel for this environment:

conda activate cell2loc_env

conda install -c bioconda -c conda-forge ipykernel

python -m ipykernel install --user --name=cell2loc_env --display-name='Environment (cell2loc_env)'

 

scanpy tutorial: spatial transcriptome data analysis-Tencent Cloud Developer Community-Tencent Cloud (tencent.com) 

scanpy_07_spatial (nbisweden.github.io)https://nbisweden.github.io/workshop-scRNAseq/labs/compiled/scanpy/scanpy_07_spatial.html