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Circadian gene identification software tools | Gene expression data analysis

Circadian rhythms are oscillations of physiology, behavior, and metabolism that have period lengths near 24 hours. In several model organisms and humans, circadian clock genes have been characterized and found to be transcription factors. Because of…
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MetaCycle
Desktop

MetaCycle

Provides two functions-meta2d and meta3d for detecting rhythmic signals from…

Provides two functions-meta2d and meta3d for detecting rhythmic signals from time-series datasets. MetaCycle is an R package for evaluating periodicity in large scale time-series datasets. MetaCycle…

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ORIOS
Desktop

ORIOS Order Restricted Inference for Oscillatory Systems

Detects rhythmic signals. Instead of using mathematical functions (e.g.…

Detects rhythmic signals. Instead of using mathematical functions (e.g. sinusoidal) to describe shape of rhythmic signals, ORIOS uses mathematical inequalities. Consequently, it is robust and not…

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BIO_CLOCK
Web

BIO_CLOCK

A machine learning method to detect molecular species that oscillate in…

A machine learning method to detect molecular species that oscillate in high-throughput circadian experiments. BIO_CLOCK estimates the time at which a particular single-time-point transcriptomic…

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BIO_CYCLE
Web

BIO_CYCLE

A machine learning method to detect molecular species that oscillate in…

A machine learning method to detect molecular species that oscillate in high-throughput circadian experiments. This method is based on BIO_CYCLE, a dataset including both synthetic and real-world…

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GeneCycle
Desktop

GeneCycle

Detects periodically expressed genes from gene expression time series data. The…

Detects periodically expressed genes from gene expression time series data. The proposed method is based on a robust spectral estimator which is incorporated into the hypothesis testing framework…

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CSR model
Desktop

CSR model Chronic Sleep Restriction model

Checks hypothesis that dynamic changes in the concentrations of both adenosine…

Checks hypothesis that dynamic changes in the concentrations of both adenosine molecules and receptors can account for changes in cognitive performance. CSR model can link the sleep homeostatic…

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PSEA
Desktop

PSEA Phase Set Enrichment Analysis

Incorporates prior knowledge into the analysis of periodic data. PSEA offers…

Incorporates prior knowledge into the analysis of periodic data. PSEA offers the ability to compare gene expression results to a nonuniform background distribution and offers the fast, dynamic…

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RAIN
Desktop

RAIN Rhythmicity Analysis Incorporating Nonparametric methods

Detects rhythms of any period and makes few assumptions about wave forms. RAIN…

Detects rhythms of any period and makes few assumptions about wave forms. RAIN uses non-parametric methods to detect rhythms in time series. RAIN deals with outliers, missing values and is optimized…

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Haystack
Web

Haystack

Compares a collection of diurnal/circadian models against microarray time…

Compares a collection of diurnal/circadian models against microarray time course data to identify cycling genes. HAYSTACK uses least-square linear regression for each gene against all model cycling…

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LSPR
Desktop

LSPR

A three-step periodicity detection algorithm. LSPR first preprocesses the raw…

A three-step periodicity detection algorithm. LSPR first preprocesses the raw time-series by removing the linear trend and filtering noise. In the second step, the method employs a Lomb–Scargle…

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periodicity
Desktop

periodicity

An analysis of variance (ANOVA) periodicity detector and its Bayesian extension…

An analysis of variance (ANOVA) periodicity detector and its Bayesian extension that can be used to discover periodic transcripts of arbitrary shapes from replicated gene expression profiles. The…

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Lomb-Scargle
Desktop

Lomb-Scargle

Provides a direct method to treat missing values and unevenly spaced time…

Provides a direct method to treat missing values and unevenly spaced time points. Lomb-Scargle is a tool for finding periodic gene expression profiles in microarray data, especially when data may be…

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ARSER
Desktop

ARSER

Combines time domain and frequency domain analysis for extracting and…

Combines time domain and frequency domain analysis for extracting and characterizing rhythmic expression profiles from temporal microarray data. ARSER employs autoregressive spectral estimation to…

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JTK_CYCLE
Desktop

JTK_CYCLE Jonckheere-Terpstra-Kendall-CYCLE

Identifies and characterizes cycling variables in large datasets. JTK_CYCLE…

Identifies and characterizes cycling variables in large datasets. JTK_CYCLE applies the JTK algorithm to alternative hypothesized group orderings corresponding to a range of user-defined period…

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robustperiodic
Desktop

robustperiodic

A general-purpose robust testing procedure for finding periodic sequences in…

A general-purpose robust testing procedure for finding periodic sequences in multiple time series data. Robustperiodic is based on a spectral estimator which is incorporated into the hypothesis…

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