CHAMOIS

Chemical Hierarchy Approximation for secondary Metabolite clusters Obtained In Silico.

Overview

CHAMOIS is a fast method for predicting chemical features of natural products produced by Biosynthetic Gene Clusters (BGCs) using only their genomic sequence. It can be used to get chemical features from BGCs predicted in silico with tools such as GECCO or antiSMASH.

Setup

Run pip install chamois-tool in a shell to download the development version from GitHub, or have a look at the Installation page to find other ways to install CHAMOIS.

Citation

CHAMOIS is scientific software, with a preprint in BioRxiv. Check the Publications page to see how to cite CHAMOIS.

Library

• User Guide
  • Installation
  • Publications
  • Contribution Guide
  • Changelog
  • Copyright Notice
• Examples
  • Basic functionalities
  • Explain a prediction
• Figures
  • Cross-validation
  • Association network
• CLI Reference
  • Inference
  • Training
  • Compound Search
  • Model Interpretation
• API Reference
  • Object model (chamois.model)
  • ORF detection (chamois.orf)
  • Domain annotation (chamois.domains)
  • Compositions (chamois.compositions)
  • Ontology (chamois.ontology)
  • Predictor (chamois.predictor)
  • ClassyFire (chamois.classyfire)

Feedback

Contact

If you have any question about CHAMOIS, if you run into any issue, or if you would like to make a feature request, please create an issue in the GitHub repository. You can also directly contact Martin Larralde via email.

Contributing

If you want to contribute to CHAMOIS, please have a look at the contribution guide first, and feel free to open a pull request on the GitHub repository.

License

This library is provided under the GNU General Public License 3.0 or later. See the Copyright Notice section for more information.

This project was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory and the Leiden University Medical Center in the Zeller team.