Get to know muon ================ `GitHub Repository `_ | `Publication `_ | `Tutorials `_ ``muon`` is a Python framework for multimodal omics analysis. While there are many features that ``muon`` brings to the table, there are three key areas that its functionality is focused on. Multimodal data containers -------------------------- ``muon`` introduces multimodal data containers (:class:`muon.MuData` class) allowing Python users to work with increasigly complex datasets efficiently and to build new workflows and computational tools around it. :: MuData object with n_obs × n_vars = 10110 × 110101  2 modalities   atac: 10110 x 100001   rna: 10110 x 10100 ``MuData`` objects enable multimodal information to be stored & accessed naturally, embrace `AnnData `_ for the individual modalities, and can be serialized to ``.h5mu`` files. :doc:`Learn more about multimodal objects ` as well as :doc:`file formats for storing & sharing them `. Multi-omics methods ------------------- ``muon`` brings multi-omics methods availability to a whole new level: state-of-the-art methods for multi-omics data integration are just a function call away. :: import muon as mu mu.tl.mofa(mdata) :doc:`Learn more about variaous multimodal integration methods ` that can be readily applied to :class:`muon.MuData` objects. Methods crafted for omics ------------------------- ``muon`` features methods for specific omics such as ATAC-seq and CITE-seq making it an extendable solution and enabling growth in an open-source environment. :: from muon import atac as ac ac.pp.tfidf(mdata.mod['atac']) from muon import prot as pt pt.pp.dsb(mdata.mod['prot']) There is :doc:`atac module ` for chromatin accessibility data and :doc:`prot module ` for CITE-seq data as well as :doc:`additional functionality ` that make individual omics analysis easier. .. toctree:: :hidden: :maxdepth: 1 :caption: Getting started notebooks/quickstart_mudata.ipynb tutorials .. toctree:: :hidden: :maxdepth: 1 :caption: Documentation install io/input io/mudata omics/uni omics/multi io/output api/index changelog