GENEFOLD

Introduction

Description

GENEFOLD is a collection of MATLAB files that implement an algorithm for the multidimensional unfolding (MDU) analysis of large data sets. Briefly said, the MDU analysis of a microarray expression dataset results in a set of coordinates for both the genes and conditions for which it holds that the Euclidean distances reflect the expression levels: the closer a condition is located to the gene, the higher the gene is expressed in that condition. The GENEFOLD algorithm can be characterized as an alternating least squares and iterative majorization algorithm with the following special features:

  • the sequence of loss function values converges to a local minimum,
  • restrictions are built in to avoid degenerate solutions,
  • the computations are based on simple mathematical operations such that an efficient algorithm is obtained that can handle large data sets in a limited amount of time.

Authors

The GENEFOLD toolbox was created by Katrijn Van Deun of the Research Group of Quantitative Psychology and Individual Differences of the Katholieke Universiteit Leuven.

References

Getting GENEFOLD

What

The installer installs GENEFOLD (m-files) on your hard disk. A description of the program and analysis options can be found in the file unfold.m

A pdf document that contains the mathematical details of the alternating least squares and iterative majorization algorithm, can be downloaded here.

Conditions

GENEFOLD is offered free of charge to anyone interested in using multidimensional unfolding models, provided that it is not used for financial profit and that you properly cite the software and the paper mentioned above. Requests to use GENEFOLD for any commercial purpose must be directed to the authors. GENEFOLD comes without any warranty of any kind. You are not allowed to redistribute a downloaded copy of GENEFOLD to others. If you want others to use GENEFOLD, refer them to this website. See here for full license information.

How

To get the software, you have to fill out your name and e-mail address in a form. After submitting that information, an e-mail containing the address where you can download the software once will be sent to you. Click here to proceed to the download area.

Communication