BioTEA, where Tea is short for Transcript Enrichment Analysis, is a pipeline for Differential Gene expression Analysis with microarray and RNA-seq data. It can download, preprocess and perform DEAs quickly, easily and in a reproducible way from the command line.

Read the publication:

Coming soon!

IMPORTANT: BioTEA works on UNIX systems. To run on Windows, use the Windows Subsystems for Linux service.

1. Install Docker. The exact process is specific to your package manager:
   • For Ubuntu, follow this guide from the official Docker documentation.
   • For MacOS, follow this guide from the official Docker documentation.
   • For Arch Linux, install with:

     pacman -Syu docker
     systemctl enable --now docker.service

     You may need administrator privileges.
   • For other distros, check your distro package manager documentation.
2. Install Python version 3.9 or over. Again, this is dependent on your package manager:
   • On Ubuntu, run apt update && apt install python.
   • On Arch linux, run pacman -Syu python.
   • On MacOS, follow this guide in the python docs.
3. Optional but strongly reccomended: Make a Python virtual environment to use bioTEA in. You can search online for a way to do this in your OS.
4. Install bioTEA with pip: pip install biotea.

If installed correctly, biotea info should give some information on the tool.

The publication provides an overview of the tool and its usage. It is a good place to start. For more information on the various commands, read the wiki.

If you run into problems, read the FAQ page on the wiki. If you still cannot solve the issue, file a bug report, detailing as much as you can your problem.

To learn how you can contribute to the tool, read the CONTRIBUTING guide.