segmenTier

A dynamic programming solution to segmentation based on maximization of arbitrary similarity measures within segments. The general idea, theory and this implementation are described in Machne, Murray & Stadler (2017) doi:10.1038/s41598-017-12401-8. In addition to the core algorithm, the package provides time-series processing and clustering functions as described in the publication. These are generally applicable where a ‘k-means' clustering yields meaningful results, and have been specifically developed for clustering of the Discrete Fourier Transform of periodic gene expression data ('circadian’ or ‘yeast metabolic oscillations’). This clustering approach is outlined in the supplemental material of Machne & Murray (2012) doi:10.1371/journal.pone.0037906, and here is used as a basis of segment similarity measures. Notably, the time-series processing and clustering functions can also be used as stand-alone tools, independent of segmentation, e.g., for transcriptome data already mapped to genes.

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