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+=================================
+Welcome to InMoose documentation!
+=================================
+
+InMoose is the INtegrated Multi Omic Open Source Environment.
+
+InMoose is intended as a comprehensive state-of-the-art Python package for -omic
+data analysis. Its current focus is on analysis of bulk transcriptomic data
+(microarray and RNA-Seq).
+It comprises Python ports of popular and recognized R tools, name ComBat
+[Johnson2007]_, ComBat-Seq [Zhang2020]_, DESeq2 [Love2014]_, edgeR [Chen2016]_,
+limma [Ritchie2015]_ and splatter [Zappia2017]_.
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Features
+
+   pycombat
+   data
+   diffexp
+
+.. toctree::
+   :maxdepth: 1
+   :caption: API
+
+   deseq
+   clustering
+   edgepy
+   limma
+   sim
+   utils
+
+Contributing to InMoose
+=======================
+
+Contribution guidelines are described in `CONTRIBUTING.md <https://github.com/epigenelabs/inmoose/blob/master/CONTRIBUTING.md>`_.
+
+Authors
+=======
+
+Contact
+-------
+To report bugs (if any?), ask for support or request improvements and new
+features, please open a ticket on our Github repository.
+You may also directly contact:
+
+Maximilien Colange at maximilien@epigenelabs.com
+
+Logo
+----
+
+The InMoose logo was designed by Léa Meunier.
+
+Citing
+======
+
+The :doc:`pycombat <pycombat>` module was previously `distributed independently <https://github.com/epigenelabs/pycombat>`_.
+
+To cite InMoose, please use one of the following references:
+
+A. Behdenna, M. Colange, J. Haziza, A. Gema, G. Appé, C.-A. Azencott and A.
+Nordor. 2023. pyComBat, a Python tool for batch effects correction in
+high-throughput molecular data using empirical Bayes methods.  *BMC
+Bioinformatics* 7;24(1):459. :doi:`10.1186/s12859-023-05578-5`
+
+M. Colange, G. Appé, L. Meunier, S. Weill, A. Nordor, A.  Behdenna. 2024.
+Differential Expression Analysis with InMoose, the Integrated Multi-Omic
+Open-Source Environment in Python. *Bioarxiv*. :doi:`10.1101/2024.11.14.623578`
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`