InstallationΒΆ

scTriangulate requires python >= 3.7. This software has been extensively tested using the conda virtual environment:

pip install sctriangulate

From source code:

# method 1: Using pip (recommened)
pip install git+https://github.com/frankligy/scTriangulate.git

# method 2: Using setuptools
git clone https://github.com/frankligy/scTriangulate
cd ./scTriangulate
conda create -n sctriangulate_env python=3.7
conda activate sctriangulate_env
pip install --upgrade setuptools==57.5.0
python setup.py install
# make sure setuptools <58, I tested setuptools=57.5.0

Note

The above approaches will take care of all dependencies for you, for the information, scTriangulate depends on

  • squidpy ==1.2.0

  • gseapy ==0.10.4

  • scrublet ==0.2.3

  • yattag

  • anytree

  • mygene ==3.2.2

A minitest is included:

cd .
pytest

# or
cd ./test
pytest mini_test.py -v