HughesLab:JTK Cycle: Difference between revisions
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[[Image:JTK_Figure_2.jpg|left|thumb|Figure 2, [http://www.ncbi.nlm.nih.gov/pubmed/20876817 Hughes et al. (2010)]<br>ROC curves showing that JTK_Cycle out-performs COSOPT and Fisher's G-test.]] | [[Image:JTK_Figure_2.jpg|left|thumb|Figure 2, [http://www.ncbi.nlm.nih.gov/pubmed/20876817 Hughes et al. (2010)]<br>ROC curves showing that JTK_Cycle out-performs COSOPT and Fisher's G-test.]] | ||
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JTK_Cycle is a non-parametric algorithm developed in collaboration with [http://scholar.google.com/citations?user=1hw5bX4AAAAJ&hl=en Professor Karl Kornacker] | JTK_Cycle is a non-parametric algorithm developed in collaboration with [http://scholar.google.com/citations?user=1hw5bX4AAAAJ&hl=en Professor Karl Kornacker] (Ohio State University) and [http://bioinf.itmat.upenn.edu/hogeneschlab/index.php Professor John Hogenesch] (University of Pennsylvania School of Medicine). Its purpose is to identify rhythmic components in large, genome-scale | ||
data sets and estimate their period length, phase, and amplitude.</p> | data sets and estimate their period length, phase, and amplitude.</p> | ||
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JTK_Cycle runs in [http://en.wikipedia.org/wiki/R_%28programming_language%29 R], a statistical language that can be downloaded [http://www.r-project.org/ here]. The scripts necessary to run JTK_Cycle are available as a .zip: [[Image: | JTK_Cycle runs in [http://en.wikipedia.org/wiki/R_%28programming_language%29 R], a statistical language that can be downloaded [http://www.r-project.org/ here]. The scripts necessary to run JTK_Cycle are available as a .zip: [[Image:JTKversion3.zip]]. This compressed file also contains a User's Guide and several example data sets. One important note: this is version 3.0 which includes improvements in the accuracy of amplitude calculations as well as confidence intervals for amplitude, and a recently added addition to improve the handling of missing data points, updated by Dr. Gang Wu. We also encourage you to explore JTK_Cycle's successor: [https://academic.oup.com/bioinformatics/article/32/21/3351/2415176/MetaCycle-an-integrated-R-package-to-evaluate MetaCycle]</p> | ||
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When publishing data analyzed by JTK_Cycle, please cite [http://www.ncbi.nlm.nih.gov/pubmed/20876817 Hughes et al. (2010) Journal of Biological Rhythms]. If you use JTK_Cycle to compare the confidence intervals of amplitude measurements, please cite [http://www.ncbi.nlm.nih.gov/pubmed/22076133 Miyazaki et al. (2011) Plos ONE]. | When publishing data analyzed by JTK_Cycle, please cite [http://www.ncbi.nlm.nih.gov/pubmed/20876817 Hughes et al. (2010) Journal of Biological Rhythms]. If you use the recently modified JTK_Cycle script to compare the confidence intervals of amplitude measurements, please also cite [http://www.ncbi.nlm.nih.gov/pubmed/22076133 Miyazaki et al. (2011) Plos ONE]. | ||
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< | If you have any difficulties getting JTK_Cycle to work on your data or need help with interpreting the results, please don't hesitate to ask: ''michael.hughes'' <at> ''wustl.edu''.</p> | ||
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Hughes Lab<br> | Hughes Lab<br> | ||
[ | [https://pulmonary.wustl.edu/ Pulmonary and Critical Care Medicine]<br> | ||
University of | Washington University School of Medicine | ||
Latest revision as of 10:16, 3 February 2017
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JTK_Cycle
ROC curves showing that JTK_Cycle out-performs COSOPT and Fisher's G-test.
JTK_Cycle is a non-parametric algorithm developed in collaboration with Professor Karl Kornacker (Ohio State University) and Professor John Hogenesch (University of Pennsylvania School of Medicine). Its purpose is to identify rhythmic components in large, genome-scale data sets and estimate their period length, phase, and amplitude.
JTK_Cycle runs in R, a statistical language that can be downloaded here. The scripts necessary to run JTK_Cycle are available as a .zip: File:JTKversion3.zip. This compressed file also contains a User's Guide and several example data sets. One important note: this is version 3.0 which includes improvements in the accuracy of amplitude calculations as well as confidence intervals for amplitude, and a recently added addition to improve the handling of missing data points, updated by Dr. Gang Wu. We also encourage you to explore JTK_Cycle's successor: MetaCycle
When publishing data analyzed by JTK_Cycle, please cite Hughes et al. (2010) Journal of Biological Rhythms. If you use the recently modified JTK_Cycle script to compare the confidence intervals of amplitude measurements, please also cite Miyazaki et al. (2011) Plos ONE.
If you have any difficulties getting JTK_Cycle to work on your data or need help with interpreting the results, please don't hesitate to ask: michael.hughes <at> wustl.edu.
Hughes Lab
Pulmonary and Critical Care Medicine
Washington University School of Medicine
