BEANIE is a python package for identification of differentially-enriched gene signatures in single-cell RNA-seq datasets. It can compare between two clinical groups of patients that share a subpopulation of cells, and calculates a biologically contextualized p-value (empirical p-value) and robustness for each gene signature. Tutorials can be found on the project wiki.
It is recommended to run BEANIE in a separate conda environment. To setup a new environment -
# Create conda environment
conda create --name beanie_env python=3.7
# Activate conda environment
conda activate beanie_env
BEANIE v1.0.0 can be installed directly via github -
pip install git+https://github.com/vanallenlab/beanie.git
(Optional) If you prefer to use jupyter-notebook or jupyter-lab for your analysis, you may have to install those separately in the newly created beanie_env after installing BEANIE.
Requirements
- python v3.7 and above.
If you use our package, please cite the preprint:
Johri S., Bi K., Titchen B., Fu J., Conway J., Crowdis J., Vokes N., Fan Z, Fong L., Park J., Liu D., He MX., Van Allen E. (2021) Dissecting tumor cellprograms through group biology estimation in clinical single cell transcriptomics. biorxiv.