Scanpro: robust proportion analysis for single cell resolution data
Scanpro is a modular tool for proportion analysis, seamlessly integrating into widely accepted frameworks in the python environment. Scanpro is fast, accurate, support datasets without replicates, and is intended to be used by bioinformatics experts and beginners.
Install
PyPi
pip install scanpro
From source:
- clone the repository
git clone https://gitlab.gwdg.de/loosolab/software/scanpro.git
- navigate to scanpro directory
cd scanpro
- then run
pip install .
Quick start
To run the tool import and call the function scanpro:
from scanpro import scanpro
out = scanpro(adata, clusters_col='clusters', conds_col='condition', samples_col='sample')
- If samples_col is not given or set to None, the dataset is assumed to be not replicated and scanpro will run the bootstrapping method.
To show the results, run
out.results.
You can plot the results by calling out.plot().
Documentation
A detailed documentation can be found here: Manual.
Citation
Alayoubi, Y., Bentsen, M. & Looso, M. Scanpro is a tool for robust proportion analysis of single-cell resolution data. Sci Rep 14, 15581 (2024). https://doi.org/10.1038/s41598-024-66381-7
Release files for scanpro 0.4.1
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| File | Size | Uploaded | Provenance | Actions |
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Release files / scanpro-0.4.1.tar.gz
| Download URL | scanpro-0.4.1.tar.gz |
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