Package: circaTime 0.99.3

Alperen Uysal

circaTime: Unified Inference of Circadian Phase from Bulk and Pseudobulk Transcriptomes

Provides a single SummarizedExperiment-based interface to published circadian phase (time-of-sample-collection) inference methods for bulk and donor-level pseudobulk transcriptomes, along with a shared cross-validation benchmarking harness, cross-dataset transfer testing, and a calibrated uncertainty layer: bootstrap and Bayesian confidence intervals validated for real coverage, a fixed or dynamically-selected clock-gene quality flag, and consensus phase estimation across every bundled engine. Does not implement a new phase-inference algorithm; unifies existing published methods that are otherwise scattered across incompatible standalone implementations.

Authors:Alperen Uysal [aut, cre]

circaTime_0.99.3.tar.gz
circaTime_0.99.3.zip(r-4.7-any)circaTime_0.99.3.zip(r-4.6-any)circaTime_0.99.3.zip(r-4.5-any)
circaTime_0.99.3.tgz(r-4.6-any)circaTime_0.99.3.tgz(r-4.5-any)
circaTime_0.99.3.tar.gz(r-4.7-any)circaTime_0.99.3.tar.gz(r-4.6-any)
circaTime_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
circaTime/json (API)

# Install 'circaTime' in R:

install.packages('circaTime', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dralperenuysal/circatime/issues

On CRAN:

software geneexpression transcriptomics sequencing microarray timecourse preprocessing

3.00 score 5 scripts 36 exports 18 dependencies

Last updated from:4790ef8d4a. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	217
linux-devel	NOTE	218
source / vignettes	OK	251
linux-release	NOTE	173
macos-release	NOTE	144
macos-oldrel	NOTE	148
windows-devel	NOTE	149
windows-release	NOTE	107
windows-oldrel	NOTE	215
wasm-release	OK	154

Exports:availableReferenceModels bayesianPhasePosterior benchmarkPhase bootstrapPhaseCI calibrationCurve circularAlign circularConcentration circularCor circularCredibleInterval circularDiff circularError circularIntervalCovers circularMAE circularMean circularQuantileInterval circularWeightedMean clockAmplitude clockCoherence coreClockGenes deriveAmplitudeThreshold estimatePhase fitMolecularTimetable fitTauFisher fitTimeSignatR fitZeitZeiger mapOrthologs phaseConfounding plotCalibration predictMolecularTimetable predictTauFisher predictTimeSignatR predictZeitZeiger show standardizeGeneIds transferPhase wrapPhase

Dependencies:abind Biobase BiocGenerics DelayedArray generics GenomicRanges IRanges lattice Matrix MatrixGenerics matrixStats S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment withr XVector

Introduction to circaTime

Rendered fromcircaTime.Rmdusingknitr::rmarkdown

Last update: 2026-08-14
Started: 2026-08-12

Help page	Topics
List the bundled reference models available to 'estimatePhase()'	availableReferenceModels
Bayesian phase posterior built on the residual-pool bootstrap	bayesianPhasePosterior
Cross-validated benchmark of phase-inference engines against ground truth	benchmarkPhase
Bootstrap confidence interval for a phase-inference engine's predictions	bootstrapPhaseCI
Empirical coverage of bootstrap intervals across nominal levels	calibrationCurve
Align unsupervised phase estimates to a reference by rotation and reflection	circularAlign
Mean resultant length of a set of phases (circular concentration)	circularConcentration
Circular-circular correlation coefficient (Jammalamadaka & SenGupta, 2001)	circularCor
Bayesian (von Mises) credible interval around a point phase estimate	circularCredibleInterval
Signed circular difference between two phases	circularDiff
Per-sample circular absolute error	circularError
Does a circular interval cover a truth value?	circularIntervalCovers
Circular mean absolute error	circularMAE
Circular mean direction	circularMean
Circular quantile interval around a set of phase draws	circularQuantileInterval
Weighted circular mean direction	circularWeightedMean
Per-sample core-clock amplitude	clockAmplitude
Dynamic per-sample circadian coherence (Phase 3 QC)	clockCoherence
The bundled core clock gene reference table	coreClockGenes
Empirically derive a low-amplitude flag threshold	deriveAmplitudeThreshold
Estimate circadian phase for new samples against a bundled reference model	estimatePhase
Fit a Molecular Timetable model from labelled training data	fitMolecularTimetable
Fit a tauFisher model from labelled training data	fitTauFisher
Fit a TimeSignatR model from labelled training data	fitTimeSignatR
Fit a ZeitZeiger model from labelled training data	fitZeitZeiger
Map gene symbols to their one-to-one ortholog in another species	mapOrthologs
Is circadian phase confounding a differential expression design?	phaseConfounding
A trained circadian phase-inference reference model	PhaseReferenceModel-class show,PhaseReferenceModel-method
Plot a calibration curve	plotCalibration
Predict circadian phase with a fitted Molecular Timetable model	predictMolecularTimetable
Predict circadian phase with a fitted tauFisher model	predictTauFisher
Predict circadian phase with a fitted TimeSignatR model	predictTimeSignatR
Predict circadian phase with a fitted ZeitZeiger model	predictZeitZeiger
Standardize gene identifiers in a SummarizedExperiment to gene symbol	standardizeGeneIds
Cross-dataset transfer benchmark of phase-inference engines	transferPhase
Wrap a phase value onto [0, period)	wrapPhase

Package: circaTime 0.99.3

circaTime: Unified Inference of Circadian Phase from Bulk and Pseudobulk Transcriptomes

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