I haven't heard of that packages....Are you hoping to find gene set clusters with relevant functions based on their expression levels across your conditions? If so, TopHat+cufflinks pipeline is a good reference.

Thank you for your answers,

in fact I find this article where they use this method : polytoumos analysis to define cluster with severel group without priori information.

Saeed et al. Science 2014

"Epigenetic programming of monocyteto-macrophage differentiation and trained innate immunity."

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polytomous model selection approach that allows for classifying genes according to

their expression pattern by considering multiple conditions simultaneously instead of generating multiple pairwise comparisons. 

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I read the sentences you emphasized in the paper. According to its quoted reference “Flexible analysis of RNA-seq data using mixed effects models”, I think the author might carry out his clustering with mmseq (https://github.com/eturro/mmseq). Perhaps that's what you want.