scTOP 1.0.0

A package for identifying cell phenotype from single-cell RNA-sequencing data.

========================================================================================= scTOP: Single-cell Type Order Parameters

A Python package for finding projections onto known cell phenotyes, given matrices of raw RNA count data. The theoretical background for this project can be found in Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003734>_ by Alex H. Lang, Hu Li, James J. Collins, and Pankaj Mehta.

A manuscript containing the technical details of applying our method to single-cell RNA-seq will be available in January 2023.

Installation

To install using pip: pip install sctop To install from github: clone or download this repo and import the module from sctop/sctop.py. See tutorial/tutorial.ipynb for an example.

(In progress!) Documentation available via Read the Docs <https://sctop.readthedocs.io/>_

Please report bugs or request new features in the Github "Issues" tab. You can also contact me directly at [e-mail].

Dependencies

• NumPy
• Pandas
• SciPy

Sources for reference databases

• Mouse Cell Atlas <http://bis.zju.edu.cn/MCA/>_