This repository has the functionality to create pseudobulk matrices, calculate pseudobulk statistics using Limma and to append this information to an anndata or multimodal data object.

Installation

After cloning the repository, pseudobulk can be installed using pip

git clone https://github.com/villani-lab/pseudobulk.git
cd pseduobulk
pip install -e .

Usage

After installation, you can import it with python

import pseudobulk as pb

pb.pseudobulk.calc_pseudobulk_stats(adata, save_path = ".", save_name = "adata_pseudobulk", save_format="zarr", write_excel_files=True)