CYCLOPS protocols

View CYCLOPS computational protocol

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CYCLOPS specifications


Unique identifier OMICS_28845
Alternative name CYCLic Ordering by Periodic Structure
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R, Julia
Computer skills Advanced
Stability Stable
tidyverse, CircStats, upsetR
Maintained Yes



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  • person_outline John Hogenesch <>

Publications for CYCLic Ordering by Periodic Structure

CYCLOPS in pipeline

PMCID: 5797448
PMID: 29404219
DOI: 10.7717/peerj.4327

[…] the median absolute deviation (mad), which is less sensitive to outliers than the standard deviation., we obtained the set of rhythmic transcripts (identified by microarray probe id) inferred by cyclops to be rhythmic in healthy human lung (). this set contains transcripts whose abundance was well described by a sinusoidal function of cyclops phase in samples from both the laval and grng […]

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CYCLOPS in publications

PMCID: 5797448
PMID: 29404219
DOI: 10.7717/peerj.4327

[…] determine whether the clock is progressing normally., a more sophisticated approach is to assume the presence of rhythms and to infer a cyclical ordering of samples, using methods such as oscope or cyclops (; ). by applying cyclops to transcriptome data from hepatocellular carcinoma, found evidence for weaker or disrupted rhythmicity of several clock genes, as well as genes involved […]

PMCID: 5666849
PMID: 29039812
DOI: 10.3390/ijms18102168

[…] metabolism and detoxification, molecular drug targets and their molecular clock control are necessary for optimally shaping the circadian drug delivery patterns to individual cts in cancer patients. cyclops i.e., cyclic ordering by periodic structure is very recently proposed algorithm by anafi and coworkers []. to develop the algorithm, large human liver and lung biopsy as well as mouse tissue […]

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CYCLOPS institution(s)
Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Divisions of Pediatric Otolaryngology and Pulmonary and Sleep Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA; Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati School of Medicine, Cincinnati, OH, USA; Department of Medicine, Center for Sleep and Circadian Neurobiology, Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA

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