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.
2 maintainers
Metadata
2 maintainers
Release files for descartes-rpa 1.2.1
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| descartes_rpa-1.2.1.tar.gz | 14.0 kB | Without provenance | Details |
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| descartes_rpa-1.2.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 30.8 kB
Release files / descartes_rpa-1.2.1.tar.gz
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Release files / descartes_rpa-1.2.1-py3-none-any.whl
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| Size | 16.8 kB |
| Tags | Python 3 |
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