A Python package for the Scalale and accurate identification condition-relevant niches from spatial omics data.
Taichi is able to automatically identify condition-relevant niches, and offers the downstream analysis based on obtained niches.
Please refer to the
- STARmap Simulation dataset Tutorial
- MERFISH Simulation dataset Tutorial (Simulation perturbated condition data link and original control data link)
- Slice-seq v2 DKD mouse disease dataset Tutorial. (Can be downloaded by
pysodb
package) - CODEX proteomics CRC dataset Tutorial. (Can be downloaded by
pysodb
package)
- Create a conda environment
conda create -n taichi-env
conda activate taichi-env
- Install the Taichi dependency
mamba install squidpy scanpy -c conda-forge (squidpy == 1.3.0 for reproducing CCI in manuscript)
pip insall pygsp ipykernel
- Install the MENDER for batch-free niches representation:
cd MENDER
python setup.py install
Install the pysodb
for efficient download processed Anndata in h5ad format (https://pysodb.readthedocs.io/en/latest/) if you want to run the DKD and CRC related analysis
We suggest using mamba
to install the dependencies.
Installing the latest version of the dependencies may lead to dependency conflicts.
If you found a bug or you want to propose a new feature, please use the issue tracker.