Installation

pip (✨recommended)

STMiner has been uploaded to PyPI, You can install STMiner via pip:

1. Create conda environment:

conda create -n stminer python=3.10

2. Activate the environment:

conda activate stminer

3. Install STMiner via pip:

pip install stminer

NOTE: If the download speed is slow, please try to specify the source

For example:

pip install stminer -i https://pypi.tuna.tsinghua.edu.cn/simple

Install a matching source checkout

Download STMiner here and unzip, then run:

python -m pip install -e .

Run this in the STMiner repository, not the documentation repository. The current source dependencies include gprofiler-official==1.0.0. New pattern-enrichment and spatial-pathway interfaces require a checkout containing those methods; an older PyPI installation may not include them. Online enrichment requires internet access; plotting an existing enrichment table does not make additional enrichment requests.