ARSER

[…] plot and the histogram of the phase value differences., the oscillation queries of the genomic bins and genes were performed using metacycle software with the rhythmic signal detection methods ars (arser), jtk (jtk_cycle) and ls (lomb-scargle). for genomic bins, we used jtk and ls methods and applied 0.05 p-value cutoff. for genic ts and nts oscillation detection, we applied the three methods […]

[…] from all three major areas of related work: classical techniques (fourier transform and autocorrelation), data-mining techniques (partial periodicity detection) and circadian rhythm detection (the arser algorithm): discrete fourier transform []: for each feature, we perform a discrete fourier transform and take the period of the peak with the largest amplitude. we take the median […]

[…] e determination of existence of a circadian biological rhythm represented in the transcriptome data [] using the r package “metacycle” that provides functions and methods (jtk_cycle, lomb-scargle and arser) for detecting rhythmic signals from time series datasets (https://cran.r-project.org/web/packages/metacycle/index.html). jtk_cycle results include the p value (pval, significative if p < 0.0 […]

[…] diurnal rhythmicity, similar to previous reports that examined circadian gene expression in wt mice (). predictively, more stringent q values reduced the number of cycling genes with both the arser (ars) and the jonckheere-terpstra-kendall (jtk) algorithms (; ). however, although similar in number, only about half the cycling transcripts from each genotype were identified in both wt […]

[…] order to compare their results with established and widely used algorithms that detect rhythmic profiles, such as jtk_cycle (hughes et al., 2010) and meta cycle (wu et al., 2016) that incorporates arser, jtk_cycle and lomb–scargle., 4) it would be interesting to compare the genes identified as rhythmic in cultured u2os cells (krishnaiah et al., 2017) with the ones identified in the current […]