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JTK_CYCLE specifications

Information


Unique identifier OMICS_13325
Name JTK_CYCLE
Alternative name Jonckheere-Terpstra-Kendall-CYCLE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Karl Kornacker <>

Publication for Jonckheere-Terpstra-Kendall-CYCLE

JTK_CYCLE in publications

 (72)
PMCID: 5908788
PMID: 29674717
DOI: 10.1038/s41467-018-03898-2

[…] division of labor for hepatic functions during the circadian cycle.fig. 2, we then investigated diurnal rhythmicity of dba of the tp-specific tfs. diurnal rhythmicity was identified according to jtk_cycle method (methods), in which 159 dbps, 80 tfs, and 59 tcs were found as diurnal rhythmic proteins (p < 0.1), accounting for 26%, 27%, and 24% of the total identifications in its functional […]

PMCID: 5904149
PMID: 29666379
DOI: 10.1038/s41467-018-03922-5

[…] 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 and used […]

PMCID: 5915959
PMID: 29713692
DOI: 10.1210/js.2018-00021

[…] ∼4% to 7% of gene transcripts follow circadian oscillations in their expression [, ]. comparison of these two studies, following re-evaluation by equivalent criteria using a nonparametric algorithm (jtk_cycle) to detect rhythmic components [], yielded ~240 common genes that exhibit statistically significant circadian expression in both studies [; see for the full list of common rhythmic genes]. […]

PMCID: 5861051
PMID: 29559663
DOI: 10.1038/s41598-018-23167-y

[…] gene expression in c. rota, we assembled a de novo transcriptome using samples collected every 4 hours over the course of 2 days during 2 lunar phases (12 time points per sampling; fig. ). employing jtk_cycle, we identified 367 tidal (p < 0.005; figs  and ; table ; file ), and 221 diel significant cyclers (figs  and ; table ; file ). significantly more transcripts peak during rising and high […]

PMCID: 5859089
PMID: 29593513
DOI: 10.3389/fnbeh.2018.00053

[…] when needed (e.g., okr). in particular, we used three independent samples for analysis and three repeated independent measurements for the gene expression experiment, with similar results. for the jtk-cycle analysis, each parameter was recorded and analyzed as previously described by r (hughes et al., ). statistical analysis was performed with graphpad prism5 software (san diego, ca, usa)., […]


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JTK_CYCLE institution(s)
Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA; Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Division of Sensory Biophysics, The Ohio State University, Columbus, OH, USA
JTK_CYCLE funding source(s)
This work was supported by the National Institute of Mental Health P50 Conte Center grant, the National Heart, Lung, and Blood Institute (NHBLI, 1R01HL097800), and Pennsylvania Commonwealth Health Research Formula Funds.

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