Statescope

Statescope is a computational framework designed to discover cell states from cell type-specific gene expression profiles inferred from bulk RNA profiles.

Installation

Using pip

The python package of Statescope is available on pip:

pip install Statescope

We tested Statescope with python => 3.10.

Using conda

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

Running a demo script

Basic Tutorial

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

Advanced Tutorial

You can also find a more advanced demo script under the tutorial folder.

jupyter notebook tutorial/AdvancedTutorial.ipynb

Documentation

Website

The documentation of Statescope is hosted on https://tgac-vumc.github.io/Statescopeweb/

System Requirements

Hardware Requirements

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.

OS Requirements

The package development version is tested on Linux operating systems. (CentOS 7 and Ubuntu 16.04).