<p>Transcriptome time-series data from a region encompassing
four genes and a regulatory upstream non-coding RNA in budding yeast.
The data set is described in more detail in the publication
Machne, Murray &amp; Stadler (2017) &lt;doi:10.1038/s41598-017-12401-8&gt;.</p>

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.

Rainer Machne

tsd: Transcriptome time-series from budding yeast.

Description

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