ExtractGEO

This is an interactive python-based datasets retriever for the GEO database

This data retriever offers a very straightforward and user-friendly way to access GEO data.
The ExtractGEO package takes inputs from the end-user and makes it easy for the user to query and download data from the Gene Expression Omnibus (GEO) database.
The GEO database contains publicly available high-throughput functional genomics data, such as microarray, next-generation sequencing

Quick Links

• About
• Technologies
• Getting Started
  • Prerequisites
  • Installation
• Usage
• Demo
• Roadmap
• Contributing
• Versioning
• Authors
• License
• Acknowledgments

About

Technologies

Built With

This project is created with:

• Python3
• GEOparse
• CircleCI
• PyInstaller

Getting Started

Prerequisites

Installation

METHOD 1

You can install the module by running python setup.py install

If you have Python installed, use pip from the terminal or a package manager such as conda:

1. Option 1: install using pip
   pip install ExtractGEO

2. Option 2: install using conda:
   conda install ExtractGEO -c conda-forge

NOTE:

• If you don’t have Python installed we recommend installing it using the Anaconda installer then running the conda install command above.
  • When installing Anaconda through the installer, make sure that the ‘add to PATH’ option is checked.

METHOD 2 From Source

If you want to use the current development version of the software either use pip to install directly from GitHub:

1. Option 1:
   pip install [github-link]

2. Option 2: Clone the repository
   cd into the repository directory and run pip install. (you may need to include sudo at the beginning of the command depending on your system).

3. Option 3: Using Git
   pip install git+https://github.com/cetienn01/extractGEO

Usage

Demo

Roadmap

See the open issues for a list of proposed features (and known issues).

Contributing

Contributions are what make the open source community such an amazing place to be learn, inspire, and create. Any contributions you make are greatly appreciated.

1. Fork the Project
2. Create your new feature branch
   git checkout -b new_feature
3. Add the amazing feature [that you've created]
   git add .
4. Commit your Changes
   git commit -m 'added an amazing feature'
5. Push to the Branch
   git push origin new_feature/AmazingFeature
6. Open a Pull Request

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Versioning

Authors

• Chris Etienne - initial work
  • twitter: @iamchrisetienne
  • email: [email protected]
• Arman Aksoy
  • twitter: armish
  • email:

See also the list of contributors who participated in this project.

Project Link : https://github.com/cetienn01/ExtractGEO

License

This project is licensed and distributed under the MIT License. See LICENSE file for more information.

Acknowledgments