Release notes#


This release comes with new features and improvements: * MOFA can be now run in the stochastic mode (SVI) using the new arguments for * MOFA model weights can be visualised with * Plotting module has gained new plots such as * It is now possible to define layers as {modality: layer} in * pysam not being installed is now handled more gracefully (#46).



MuData is now provided as a separate package. Since this release, mudata is a hard dependency of muon. Making the codebase more modular, this will also help developing tools around MuData that do not depend on scanpy or muon.

We fixed a few things including reading .h5mu files in backed mode when modalities have .raw attributes (this is live in the mudata library), SNF functionality ( and colouring plots by var_names that are present in .raw but not in the root AnnData object.

We also introduced some new features for the ATAC module including:

  • handling fragments files with barcodes different than obs_names and

  • supporting atac_peak_annotation.tsv files produced by Cell Ranger ARC 2.0.0.


Initial muon release with MuData (muon.MuData), atac and prot submodules (muon.atac and muon.prot), and multi-omics integration with MOFA ( and WNN (muon.pp.neighbors()).