Welcome to COMMAND>_’s documentation!

COMMAND>_ is a web-based application used to download, collect and manage gene expression data from public databases.

Main features are.

  • Easy installation and update using Docker Compose technology.
  • Graphical User Interface (GUI) for parsing and importing gene expression data.
  • Default Python scripts for easy parsing/importing of the most common microarray platforms (Affymetrix, Nimblegen, two-colors, etc.) and dedicated scripting editor for allowing flexible importing of any kind of gene expression data.
  • Automatic pre-processing (downloading, trimming, mapping and counting) of bulk RNA-Seq data.
  • Exporting of the collected data.


Give it a try on https://command.fmach.it:4242 using:

  • username: guest
  • password: demo

Check out the Use Cases!

Contribute & Support

Use the GitHub Push Request and/or Issue Tracker.


To send me an e-mail about anything else related to COMMAND>_ write to email


The project is licensed under the GPLv3 license.

How to cite

If you find COMMAND>_ useful for your work please cite

Moretto, M., Sonego, P., Villaseñor-Altamirano, A. B., & Engelen, K. (2019). First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_. BMC bioinformatics, 20(1), 54. ISO 690