# Welcome to OpenOmics's documentation!

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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

```