muon v0.1.7

Fixes

Important

In this release, there are some functions where the bugfixes and improvements led to changes in their behavior. This is why in some instances, this version might produce different outputs when compared to the previous versions. See e.g. #147.

• Enable compatibility of in-place filtering with the latest anndata (#148)
• Fix tfidf when using data from a layer (#147)
• Fix custom chromosome names in count_fragments_features (#140)
• Prepare to count unique fragments in count_fragments_features from the next version (see #110)
• Improve mu.pl.scatter()

🐛 → 🦋

muon v0.1.6

Fixes and enhancements

• ✨ extend _l2norm for sparse inputs (#114)
• improve data type handling for MOFA (#112)
• improve compatibility with the recent scanpy versions (#136)

muon v0.1.5

Fixes

• fix handling and saving colour palettes in MuData for categorical and continuous variables (#109)
• fix when using sparse matrices in the MOFA interface to combine modalities with missing samples (#106)
• fix error messages (#95) and mixing metadata and features (#96) when plotting across modalities

muon v0.1.4

Improvements and fixes

• mu.pp.intersect_obs now works for modalities that have no .X (#93)
• mu.pl.embedding now saves the colour palette in .uns
• ac.pl.fragment_histogram and mu.pl.histogram now have save/show arguments (#101)
• ac.tl.count_fragments_features now has a stranded argument
• ac.tl.nucleosome_signal now works on more pysam setups (#105)
• support for numpy 1.24 and newer scanpy versions

muon v0.1.3

Tools

• MOFA can be now run in the stochastic mode (SVI) using the new arguments for muon.tl.mofa (#47)
• Model weights can be visualised with mu.pl.mofa_loadings

Plotting

• Plotting module has gained new plots such as mu.pl.scatter (#48)
• It is now possible to define layers as {modality: layer} in mu.pl.scatter

ATAC module

• pysam not being installed is now handled more gracefully (#46)
• Improvements to the TF-IDF normalisation interface including view handling (#88)

General

• sklearn vs scikit-learn dependency issue is fixed (#91)

muon v0.1.2

This is a point release with fixes. Consecutive in-place filtering now works as expected (#43).

muon v0.1.1

An update to muon with fixes and improvements. MuData has found a new home in a standalone package.

muon v0.1.0

Initial muon release with MuData, atac and prot modules, and multi-omics integration with MOFA and WNN.