.. MIRA documentation master file, created by
   sphinx-quickstart on Tue Jan  4 12:00:13 2022.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

.. image:: _static/mira_logo.png
  :width: 400
  :alt: MIRA
  :align: center

------------

.. container :: home-content

     .. code-block :: bash
     
          conda install -c conda-forge -c bioconda -c liulab-dfci mira-multiome

     **Multimodal models for Integrated Regulatory Analysis**, or MIRA,  is a python package for analyzing
     the dynamic processes of gene regulation using single-cell multiomics datasets. 

     MIRA works on top of `Scanpy <https://scanpy.readthedocs.io/en/stable/>`_ and `Anndata <https://anndata.readthedocs.io/en/latest/>`_
     to provide a rich, comprehensive framework integrating accessibility and expression data for more insights
     into your data. MIRA includes methods for:

     .. panels::
          :card: + text-center
          :img-top-cls: panel-height
          :body: p-0

          ---
          :img-top: _static/topic_model_pictograph.svg

          +++
          .. link-button:: notebooks/tutorial_topic_model_tuning_full
               :type: ref
               :text: Multimodel Topic Modeling
               :classes: btn-link stretched-link font-weight-bold
          ---
          :img-top: _static/joint_representation.png

          +++
          .. link-button:: notebooks/tutorial_joint_representation
               :type: ref
               :text: Constructing a Joint Representation
               :classes: btn-link stretched-link font-weight-bold

          ---
          :img-top: _static/enrichment_example.png
          
          +++
          .. link-button:: notebooks/tutorial_topic_analysis
               :type: ref
               :text: Regulator and Functional Enrichment
               :classes: btn-link stretched-link font-weight-bold

          ---
          :img-top: _static/stream_example.png
          +++
          .. link-button:: notebooks/tutorial_mira.time
               :type: ref
               :text: Pseudotime Trajectory inference
               :classes: btn-link stretched-link font-weight-bold

          ---
          :img-top:  _static/rp_model_plot.png
          +++
          .. link-button:: notebooks/tutorial_cisregulatory_modeling
               :type: ref
               :text: Regulatory Potential Modeling
               :classes: btn-link stretched-link font-weight-bold

          ---
          :img-top:  _static/chromatin_differential.png
          +++
          .. link-button:: notebooks/tutorial_NITE_LITE_modeling
               :type: ref
               :text: Finding NITE regulation
               :classes: btn-link stretched-link font-weight-bold

     \.\.\. And more! Check out the `MIRA preprint <https://www.biorxiv.org/content/10.1101/2021.12.06.471401v1.full.pdf>`_ on bioarxiv. 
     Also, see :doc:`getting_started` for installation and data preparation instructions.

------------

.. container :: hidden

     Docs
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.. toctree::
     :maxdepth: 2
     :hidden:

     getting_started
     tutorials
     api
     faq
     news
