Release notes

v0.1.6

• Compatibility with scanpy 1.10

v0.1.5

This release comes with fixes:

• for handling and saving colour palettes in MuData for categorical and continuous variables in muon.pl.embedding(),

• for using sparse matrices in the MOFA interface to combine modalities with missing samples in muon.tl.mofa(),

• for error messages and mixing metadata and features when plotting across modalities with muon.pl.embedding().

v0.1.4

This release comes with improvements and fixes:

• muon.pp.intersect_obs() now works for modalities that have no .X

• muon.pl.embedding() now saves the colour palette in .uns

• muon.atac.pl.fragment_histogram() and muon.pl.histogram() now have save/show arguments

• muon.atac.tl.count_fragments_features() now has a stranded argument

• muon.atac.tl.nucleosome_signal() now works on more pysam setups

• support for numpy 1.24 and newer scanpy versions

v0.1.3

This release comes with new features and improvements:

• MOFA can be now run in the stochastic mode (SVI) using the new arguments for muon.tl.mofa().

• MOFA model weights can be visualised with muon.pl.mofa_loadings().

• Plotting module has gained new plots such as muon.pl.scatter().

• It is now possible to define layers as {modality: layer} in mu.pl.embedding().

• Improvements to the TF-IDF normalisation interface including view handling.

• Dependencies are handled better now such as pysam and scikit-learn.

v0.1.2

• In-place filtering functions (muon.pp.filter_obs() and muon.pp.filter_var()) can be now run one after another without requiring muon.MuData.update()).

v0.1.1

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 (muon.tl.snf()) 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.

v0.1.0

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