added info

docs/source/index.rst

@@ -1,30 +1,84 @@
-############
-Introduction
-############
+NetworkCommons
+==============================================================
 
-Created from a project template. Please write the docs of your project here,
-and remove the parts below (or edit ``README.rst`` in the project root).
+|MainBuild| |Issues| |PyPIDownloads| |Docs| |Codecov|
 
-.. include:: ../../README.rst
+|Conda| |CondaDownloads|
 
-#########
-Reference
-#########
+.. |MainBuild| image:: https://github.com/saezlab/networkcommons/actions/workflows/main.yml/badge.svg
+   :target: https://github.com/saezlab/networkcommons/actions
+
+.. .. |Issues| image:: https://img.shields.io/github/issues/saezlab/networkcommons.svg
+..    :target: https://github.com/saezlab/networkcommons/issues/
 
-project_name
-============
+.. .. |PyPIDownloads| image:: https://static.pepy.tech/badge/decoupler
+..    :target: https://pepy.tech/project/decoupler
+   
+.. .. |Docs| image:: https://readthedocs.org/projects/networkcommons/badge/?version=latest
+..    :target: https://networkcommons.readthedocs.io/en/latest/?badge=latest
 
-.. automodule:: project_name
-   :members:
+.. |Codecov| image:: https://codecov.io/github/saezlab/networkcommons/graph/badge.svg?token=RH438ALJC2
+   :target: https://codecov.io/gh/saezlab/networkcommons
 
-###########################
-Indices, Tables, and Search
-###########################
+.. .. |Conda| image:: https://img.shields.io/conda/vn/conda-forge/decoupler-py.svg
+..    :target: https://anaconda.org/conda-forge/decoupler-py
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+.. .. |CondaDownloads| image:: https://img.shields.io/conda/dn/conda-forge/decoupler-py.svg
+..    :target: https://anaconda.org/conda-forge/decoupler-py
 
+``NetworkCommons`` is a package which allows users to download data and prior knowledge to perform static network inference using different methodologies. The package also provides different visualization and evaluation strategies.
+
+.. .. figure:: graphical_abstract.png
+..    :height: 500px
+..    :alt: decoupler’s workflow
+..    :align: center
+..    :class: no-scaled-link
+
+..    decoupler contains a collection of computational methods that coupled with 
+..    prior knowledge resources estimate biological activities from omics data.
+
+.. Check out the `Usage <https://decoupler-py.readthedocs.io/en/latest/notebooks/usage.html>`_ or any other tutorial for further information.
+
+.. If you have any question or problem do not hesitate to open an `issue <https://github.com/saezlab/decoupler-py/issues>`_.
+
+.. scverse
+.. -------
+.. ``decoupler`` is part of the `scverse <https://scverse.org>`_ ecosystem, a collection of tools for single-cell omics data analysis in python.
+.. For more information check the link.
+
+License
+-------
+The data redistributed by OmniPath does not have a license, each original resource carries their own. 
+`Here <https://omnipathdb.org/info>`_ one can find the license information of all the resources in OmniPath.
+
+.. Citation
+.. -------
+.. Badia-i-Mompel P., Vélez Santiago J., Braunger J., Geiss C., Dimitrov D., Müller-Dott S., Taus P., Dugourd A., Holland C.H., 
+.. Ramirez Flores R.O. and Saez-Rodriguez J. 2022. decoupleR: ensemble of computational methods to infer biological activities 
+.. from omics data. Bioinformatics Advances. https://doi.org/10.1093/bioadv/vbac016
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 1
+   :hidden:
+   :caption: Main
+
+   installation
+   api
+   release_notes
+   reference
+
+.. toctree::
+   :maxdepth: 1
+   :hidden:
+   :caption: Vignettes
+
+   notebooks/a_simple_example
+   notebooks/MOON
+   notebooks/progeny
+   notebooks/dorothea
+   notebooks/msigdb
+   notebooks/pseudobulk
+   notebooks/spatial
+   notebooks/bulk
+   notebooks/benchmark
+   notebooks/translate