Statescope is a computational framework designed to discover cell states from cell type-specific gene expression profiles inferred from bulk RNA profiles.
The python package of Statescope is available on pip:
pip install Statescope
We tested Statescope with python => 3.10.
In case the pip installation gives you problems, you can also use the environment.yaml file provided on this Github.
conda env create -f environment.yaml
conda activate Statescope
This install Statescope version 1.0.8 with python 3.10.19
You can find an basic demo script under the tutorial folder.
You can open the script using the command below after installing Statecope:
jupyter notebook tutorial/BasicTutorial.ipynb
You can also find a more advanced demo script under the tutorial folder.
jupyter notebook tutorial/AdvancedTutorial.ipynb
The documentation of Statescope is hosted on https://tgac-vumc.github.io/Statescopeweb/
Statescope can run on the minimal computer spec, such as Binder (1 CPU, 2GB RAM on Google Cloud), when data size is small. However, Statescope can significantly benefit from the larger amount of CPUs and RAM and can leverage GPU hardware.
The package development version is tested on Linux operating systems. (CentOS 7 and Ubuntu 16.04).