question: Which comparisons demonstrate the applicability of StereoGene in regulatory genomics?
answer: StereoGene rapidly estimates genome-wide correlation among pairs of genomic features. These features may represent high-throughput data mapped to reference genome or sets of genomic annotations in that reference genome. StereoGene enables correlation of continuous data directly, avoiding the data binarization and subsequent data loss. Correlations are computed among neighboring genomic positions using kernel correlation. Representing the correlation as a function of the genome position, StereoGene outputs the local correlation track as part of the analysis. StereoGene also accounts for confounders such as input DNA by partial correlation. Numerous comparisons of ChIP-Seq datasets from the Human Epigenome Atlas and FANTOM CAGE demonstrate the wide applicability of StereoGene in regulatory genomics.