Release notes ============= .. contents:: :local: :depth: 3 .. toctree:: :maxdepth: 10 * 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 :func:`muon.tl.mofa` * MOFA model weights can be visualised with :func:`mu.pl.mofa_loadings` * Plotting module has gained new plots such as :func:`muon.pl.scatter` * It is now possible to define layers as `{modality: layer}` in :func:`mu.pl.embedding` * `pysam` not being installed is now handled more gracefully (#46). v0.1.2 ------ * In-place filtering functions (:func:`muon.pp.filter_obs` and :func:`muon.pp.filter_var`) can be now run one after another without requiring :func:`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 (:func:`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`` (:class:`muon.MuData`), ``atac`` and ``prot`` submodules (:mod:`muon.atac` and :mod:`muon.prot`), and multi-omics integration with ``MOFA`` (:func:`muon.tl.mofa`) and ``WNN`` (:func:`muon.pp.neighbors`).