Usage

Installation

Install the python package with pip directly from github as:

pip install git+https://github.com/KellisLab/scdemon

For a fresh install, or if version number hasn’t changed, first run: pip uninstall scdemon

Alternatively, install by cloning the directory as:

git clone git@github.com:KellisLab/scdemon.git
pip install ./scdemon

A minimal conda environment for this package includes:

# Minimal:
conda create -n scdemonpy -c conda-forge numpy pandas scipy igraph umap-learn leidenalg scanpy seaborn matplotlib

# If you want to run GO enrichment:
conda install -n scdemonpy -c bioconda gprofiler-official

The full list of dependencies is as follows:

# Core:
numpy, pandas, scipy, igraph, umap-learn,
leidenalg, scanpy, seaborn, matplotlib

# Optional:
anndata, gprofiler-official, adjustText