pathsingle 0.2.0

PathSingle is a Python package for pathway analysis of single-cell RNA-seq data.

PathSingle: A Biochemical Pathway Analysis Tool for Single-Cell Data

Overview

PathSingle is a Python-based pathway analysis tool tailored for single-cell data analysis. It employs a unique graph-based algorithm to enable the analysis of diverse cellular states, such as T cell subtypes. Designed to be open-source, extensible, and computationally efficient, PathSingle provides researchers with a versatile framework for uncovering biologically meaningful insights from high-dimensional single-cell transcriptomics data.

Key Features

• Tailored for single-cell RNA-seq data analysis
• Unique graph-based algorithm for pathway analysis
• Efficient classification of diverse cellular states
• Open-source and extensible
• Computationally efficient

Installation

pip install pathsingle

Or simply clone this repository using git clone command.

Quick Start

anndata = sc.read('./data/activity_df.csv', delimiter=',', cache=False)
calc_activity(anndata)

Usage

For detailed usage instructions, please refer to the scripts and notebooks in the pathsingle folder.

Single Cells Benchmark Readme

Feature Reduction Notebook

The pathway_db subfolder contains scripts for building and customizing the pathways database.

• kegg: Scripts for downloading pathways from KEGG PATHWAY database and building the existing PathSingle database pathway_relations.csv.
• reactome: Scripts for downloading and building a new PathSingle pathway_relations.csv database using Reactome Pathway database.
• pathwaycommon: Scripts for downloading and building a new PathSingle pathway_relations.csv database using Pathway Commons integrated database.

Supported Pathways

PathSingle currently supports 357 curated pathways. Click the link to view the full list. List of supported pathways.

Contributing

We welcome contributions! Please see our Contributing Guidelines for more information on how to get involved.

License

PathSingle is available under the MIT license. See the LICENSE file for more details.

Support

For questions, issues, or feature requests, please open an issue on our GitHub repository.

For additional support, contact: zurkin at yahoo dot com.

Acknowledgments

We thank the scientific community for their valuable feedback and contributions to this project.