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Eric Bonnet edited this page Aug 13, 2020 · 11 revisions

Welcome

Welcome to the Lemon-Tree project. Lemon-Tree is a "one-stop shop" software suite for module network inference that aims to make module network methods available to a broader community of users while simultaneously facilitating and encouraging collaborations between developers. Module networks are probabilistic graphical models which consist of modules of coregulated genes and their regulatory programs, and they can be inferred from integrated genomic data compendia (including gene expression, microRNA expression, copy number variation, and more) measured in a large number of individuals or experimental conditions.

Download

Binaries (Java jar, Javadoc and libraries packages) for the latest release (and for older versions) of lemon-tree are available from our Google drive repository.

Release info

Introduction

For the public release of Lemon-Tree (version 3 and above) we have ported all of the data structures and algorithms from our previous tool LeMoNe and developed a number of extensions and improvements, including:

  • A complete Java implementation of all steps in the model learning process with uniform input/output format.
  • A novel algorithm based on rigorous algebraic results to reconstruct overlapping consensus clusters from an ensemble of clustering results, each of which may be overlapping or not.
  • Novel methods to incorporate discrete regulators (e.g. eQTLs, CNVs, clinical grades) into the model, thereby greatly expanding the number and types of data that can be integrated.
  • Novel methods to visualise co-expression modules and their predicted regulators allowing for better interpretation and hypothesis generation.

Where to go next?

  • Start with the step-by-step tutorial.
  • Read more about module networks and their applications in one of the many publications compiled in the module network bibliography.
  • Compare features of Lemon-Tree to existing module network software tools in our comparison table.
  • Join the discussion group if the above does not answer all your questions.
  • And last but not least, if you are a developer and you are interested in porting your existing module network code to the Lemon-Tree project or you have ideas for further project extensions, or want to contribute for testing and documentation, please do not hesitate to clone this project, make modifications and send us a pull request!

Please cite

The Lemon-Tree software is described in the following publication, part of the PLOS Computational Biology Software collection:

Please cite this manuscript if you used Lemon-Tree in your research, in addition to any other relevant publications from the module network bibliography.

Who are we?

Current project members/developers are:

  • Eric Bonnet is a senior research engineer and group leader at the French CEA/CNG institute.
  • Tom Michoel is a professor and group leader at the University of Bergen.

Parts of the code ported from LeMoNe were developed by:

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