Single-Cell pathway annotation pipeline

Single-Cell sequencing is a new methodology that provides high-resolution data to understand individual cells. Applied to RNA sequencing, it can reveal a multitude of relevant information, such as identifying different cell types within a sample and RNA velocity to understand cell fate. The possibility to query individual cells permits a fine-grained analysis compared to conventional NGS (Next Generation Sequencing) methods.

Reactome is a “free, online, and open-source database” that stores pathway data from various organisms, such as genes that make up the pathways and hierarchy mappings. Leveraging on this curated data and using single-cell resources from descartes database, we can enhance this data by annotating which pathways each identified cluster represents.

This project aims to create a dockerized python pipeline to extract pathway activity from single-cell clusters in a systematic manner, annotating each cluster with which pathway it represents.