Installation

Our tools should be installed on a Linux/Windows system with Python3.8+.

Installing with a ‘package manager’

We strongly recommend your installation executed in an isolated conda environment, so firstly run:

conda create --name spagrn python=3.8 # The env name could be set arbitrarily.

Then get into the environment you build:

conda activate spagrn

To install the latest version of SpaGRN via PyPI:

pip install spagrn==1.0.7

Or install by conda:

conda install -c bioconda spagrn

Notice: If you install via conda, you will need to install the following dependencies separately:

pyscenic==0.12.1
hotspotsc==1.1.1
arboreto
ctxcore>=0.2.0

SpaGRN can be imported as:

from spagrn import InferNetwork as irn

from spagrn import plot as prn

Dependencies:

anndata==0.8.0
pandas<2.0.0,>=1.3.4
scanpy==1.9.1
seaborn
matplotlib
pyscenic==0.12.1
hotspotsc==1.1.1
scipy
numpy
dask
arboreto
ctxcore>=0.2.0
scikit-learn

Development Mode

Use the latest version of dev branch on Github, you need to clone the repository and enter the directory:

git clone -b dev https://github.com/BGI-Qingdao/SpaGRN.git

cd SpaGRN

Install each module of interest via its own instructions

Troubleshooting

Possible installation failed due to some factors:

Version of Python

Make sure you are working on Python3.8.

Conflicts of dependencies

Find out packages that lead to failures, then create a new requirements.txt of them and run:

pip install -r requirements.txt