descartes_rpa

Python pipeline to extract pathway activity from single-cell clusters in a systematic manner, annotating each cluster with which pathway(s) it represents.

Pathways are annotated by extracting the differentialy expressed genes found in each clusters. Then, the pathways represented by these genes are retrieved using the Reactome analysis tools (explained here).

Quickstart

Here you can see examples of Single-Cell cluster pathway annotation using a 10x Genomics data set from the main Scanpy tutorial, or an example on Mouse Single-Cell data from the Scanpy hematopoiesis in mouse tutorial.

You can also check examples using the Descartes data set from human Single-Cell tissues, such as Pancreas and Liver.

Installing

Locally

Install the module using pip

pip install descartes_rpa

Docker

Build image

docker-compose build descartes_rpa

Run the image

docker-compose run --rm descartes_rpa

Descartes pathway data

Single-Cell cluster pathways data for each tissue in the descartes Human Gene Expression During Development database can be found in this link.