simPATHy: a new method for simulating data from perturbed biological PATHways

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Abstract

Summary:

In the omic era, one of the main aims is to discover groups of functionally related genes that drive the difference between different conditions. To this end, a plethora of potentially useful multivariate statistical approaches has been proposed, but their evaluation is hindered by the absence of a gold standard. Here, we propose a method for simulating biological data - gene expression, RPKM/FPKM or protein abundances - from two conditions, namely, a reference condition and a perturbation of it. Our approach is built upon probabilistic graphical models and is thus especially suited for testing topological approaches.

Availability and Implementation:

The simPATHy is an R package, it is open source and freely available on CRAN.

Contacts:

elisa.salviato.2@studenti.unipd.it or chiara.romualdi@unipd.it

Supplementary information:

Supplementary data are available at Bioinformatics online.

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