DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database. Read the documentation DISCOtoolkit. It provides the following functions:
- Filter and download DISCO data based on sample metadata and cell type information
- CELLiD: cell type annotation
- scEnrichment: geneset enrichment using DISCO DEGs
Dependency Requirements:
- Numpy >= 1.21.6
- Pandas >= 1.4.2
- Scanpy >= 1.9.3
- Scipy >= 1.8.0
- joblib >= 1.1.0
- pandarallel >= 1.6.5
The DISCOtoolkit can be easily installed in the current Python environment using pip:
pip install discotoolkit
we recommend to install miniconda first and install discotoolkit in virtual env
conda create --name disco python=3.8
conda activate disco
conda install ipykernel
python -m ipykernel install --user --name disco --display-name "disco"
python -m pip install discotoolkit # adding -U for installing the latest version
Example in Jupyter notebook.
please select disco as the kernel for running the jupyter notebook