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