Statescope framework to uncover cell states from bulk RNA-seq and DNA-seq data
Project description
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.
Running a demo script
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
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).
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