Release notes#

v0.1.7 #

Enable compatibility of in-place filtering with the latest anndata releases
muon.pp.tfidf() when using data from a layer
Fix custom chromosome names in muon.atac.tl.count_fragments_features()
Prepare to count unique fragments in muon.atac.tl.count_fragments_features() from the next version
Improve muon.pl.scatter()

v0.1.6 #

Compatibility with scanpy 1.10
Extend _l2norm to sparse inputs.

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()).

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()).

Release notes

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