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+# Welcome to OpenOmics's documentation!
+
+[![PyPI version](https://badge.fury.io/py/openomics.svg)](https://badge.fury.io/py/openomics)
+[![Documentation Status](https://readthedocs.org/projects/openomics/badge/?version=latest)](https://openomics.readthedocs.io/en/latest/?badge=latest)
+[![OpenOmics](https://github.com/JonnyTran/OpenOmics/actions/workflows/python-package.yml/badge.svg?branch=master)](https://github.com/JonnyTran/OpenOmics/actions/workflows/python-package.yml)
+[![codecov](https://codecov.io/gh/JonnyTran/OpenOmics/branch/master/graph/badge.svg?token=WAN3PJwM42)](https://codecov.io/gh/JonnyTran/OpenOmics)
+
+This Python package provide a series of tools to integrate and query the genomics, transcriptomics, proteomics, and
+clinical data (aka, the multi-omics data). With scalable data-frame manipulation tools, OpenOmics facilitates the common
+coding tasks when preparing data for RNA-seq bioinformatics analysis.
+
+## Features
+
+- Provides a bioinformatics workflow to generate integrative results from multi-omics data.
+- Facilitates integration of various bio-databases, multi-omics expression, genomics, and clinical data.
+- Highly flexible to different data types and missing data.
+- Provides researchers with means to consistently store and explore their experimental datasets.
+- Enables scalable performance with parallel computing, while easily configurable to deploy on both single machine and a
+  cluster.
+
+## Table of Content
+
+```{toctree}
+:maxdepth: 2
+:caption: Using OpenOmics Python API
+:name: mastertoc
+installation
+usage/getting-started
+usage/import-your-dataset
+usage/annotate-external-databases
+usage/network-data
+usage/preprocess-downstream-analysis
+```
+
+```{toctree}
+:maxdepth: 1
+:caption: API Reference
+
+modules/openomics.multiomics
+modules/openomics.annotate
+modules/openomics.database.annotation
+modules/openomics.database.sequence
+modules/openomics.database.interaction
+modules/openomics.database.disease
+modules/openomics.database.ontology
+modules/openomics.utils
+```
+
+
+```{toctree}
+:maxdepth: 1
+:caption: MISC
+
+misc/faq
+```
+
+
+```{toctree}
+:maxdepth: 1
+:caption: Contributing and releases
+
+contributing
+history
+```