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Analyzing gene perturbation screens with nested effects models in R and bioconductor

Fröhlich, H. ; Beissbarth, T. ; Tresch, A. ; Kostka, D. ; Jacob, Juby ; Spang, Rainer ; Markowetz, F.


Nested effects models (NEMs) are a class of probabilistic models introduced to analyze the effects of gene perturbation screens visible in high-dimensional phenotypes like microarrays or cell morphology. NEMs reverse engineer upstream/downstream relations of cellular signaling cascades. NEMs take as input a set of candidate pathway genes and phenotypic profiles of perturbing these genes. NEMs ...


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