xcore: an R package for inference of gene expression regulators - BMC Bioinformatics

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xcore: an R package for inference of gene expression regulators - BMC Bioinformatics
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An article published in BMCBioInformatics discusses xcore: A simple analytical framework for gene expression modeling using linear models that can be easily incorporated into differential expression analysis pipelines.

The authors declare that they have no competing interests. EA took a position with GSK during the submission of this manuscript. GSK was not involved at any stage of the work presented here and there is no conflict of interest related to GSK for this work. BK took a position with AstraZeneca R&D during the submission of this manuscript.

Heatmap on the right depicts TF activities estimated using previously published microarray data from the TGFβ induced EMT experiment performed on A-549 cell lines. The TF activities were calculated in the reference to 0 h time point. Only the top-scoring ChIP-Atlas signatures are shown. Grey color designates NA values. Boxplots showing Rvalues for gene expression prediction models constructed using different molecular signature sets: Motif based and ChIP-seq based .

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