--- a
+++ b/docs/index.rst
@@ -0,0 +1,58 @@
+|Stars| |PyPI| |PyPIDownloads| |Bioconda| |Docs|
+
+MultiVelo - Velocity Inference from Single-Cell Multi-Omic Data
+===============================================================
+
+Single-cell multi-omic datasets, in which multiple molecular modalities are profiled 
+within the same cell, provide a unique opportunity to discover the interplay between 
+cellular epigenomic and transcriptomic changes. To realize this potential, we developed 
+**MultiVelo**, a mechanistic model of gene expression that extends the popular RNA velocity 
+framework by incorporating epigenomic data.
+
+MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate 
+parameters of gene regulation, providing a quantitative summary of the temporal relationship 
+between epigenomic and transcriptomic changes. Fitting MultiVelo on single-cell multi-omic 
+datasets revealed two distinct mechanisms of regulation by chromatin accessibility, quantified 
+the degree of concordance or discordance between transcriptomic and epigenomic states within 
+each cell, and inferred the lengths of time lags between transcriptomic and epigenomic changes.
+
+Check out the :doc:`usage` section for further information.
+
+
+.. toctree::
+   :caption: Main
+   :maxdepth: 1
+   :hidden:
+
+   usage
+   api
+
+.. toctree::
+   :caption: Demo
+   :maxdepth: 1
+   :hidden:
+
+   MultiVelo_Demo
+   MultiVelo_Fig2
+   MultiVelo_Fig3
+   MultiVelo_Fig4
+   MultiVelo_Fig5
+   MultiVelo_Fig6
+   adam_example
+   neural_net_example
+
+
+.. |Stars| image:: https://img.shields.io/github/stars/welch-lab/multivelo?logo=GitHub&color=yellow
+   :target: https://github.com/welch-lab/multivelo/stargazers
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/multivelo?logo=PyPI
+   :target: https://pypi.org/project/multivelo
+
+.. |PyPIDownloads| image:: https://pepy.tech/badge/multivelo
+   :target: https://pepy.tech/project/multivelo
+
+.. |Bioconda| image:: https://img.shields.io/conda/dn/bioconda/multivelo?logo=Anaconda
+   :target: https://anaconda.org/bioconda/multivelo
+
+.. |Docs| image:: https://readthedocs.org/projects/multivelo/badge/?version=latest
+   :target: https://multivelo.readthedocs.io