A Python package for the Scalale and accurate identification condition-relevant niches from spatial omics data.

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Preprint

Taichi is able to automatically identify condition-relevant niches, and offers the downstream analysis based on obtained niches.

Getting started

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)

Installation

1. Create a conda environment

conda create -n taichi-env
conda activate taichi-env

2. Install the Taichi dependency

mamba install squidpy scanpy -c conda-forge (squidpy == 1.3.0 for reproducing CCI in manuscript)
pip insall pygsp ipykernel

3. 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.

Contribution

If you found a bug or you want to propose a new feature, please use the issue tracker.