Installation guide

Main package

The scglue package can be installed either via conda:

conda install -c defaults -c pytorch -c bioconda -c conda-forge -c scglue scglue

Or via pip:

pip install scglue


To avoid potential dependency conflicts, installing within a conda environment is recommended.

Optional dependencies

Some functions in the scglue package use metacell aggregation via k-Means clustering, which can receive significant speed up with the faiss package.

You may install faiss following the official guide.

Now you are all set. Proceed to tutorials for how to use the scglue package.