Links between modalities in mudata
mulink models feature relationships between mudata modalities as directed acyclic graph. To work with this mapping, it extends the namespace of mudata with a custom link attribute. The individual functionalities are implemented as accessors to this namespace.
import mudata as md
import mulink # registers the `link` namespace on mudata
from scipy.sparse import csr_matrix
# minimal example
mdata = mulink.simulate.hierarchical_mudata(n_mod=3)
assert isinstance(mdata, md.MuData)
assert "feature_mapping" in mdata.varp.keys()
assert hasattr(mdata, "link")
# add linkage matrix
mdata.link.add_link(csr_matrix(...))
# querying
mdata.link.query.descendants("mod0-0")
mdata.link.query.ancestors("mod2-0")
# plotting
mdata.link.pl.graph()For more information, please refer to the documentation, in particular, the API documentation and the Design Document.
You need to have Python 3.11 or newer installed on your system. If you don't have Python installed, we recommend installing uv.
There are several alternative options to install mulink:
Install the latest release of mulink from PyPI:
pip install mulinkmulink is under active development. You can install development versions via:
pip install git+https://github.com/lucas-diedrich/mulink.git@mainSee the changelog.
If you found a bug or have an idea for a new feature, please use the issue tracker.
This project was started at the scverse proteomics hackathon in Berlin 2026. Comparable features are implemented in the QFeatures package in R.
scverse proteomics working group 2026. mulink.