Package: circaTime
Type: Package
Title: Unified Inference of Circadian Phase from Bulk and Pseudobulk
        Transcriptomes
Version: 0.99.3
Authors@R: person("Alperen", "Uysal", role = c("aut", "cre"),
    email = "dralperenuysal@gmail.com",
    comment = c(ORCID = "0000-0003-3777-6411"))
Description: 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.
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
biocViews: Software, GeneExpression, Transcriptomics, Sequencing,
        Microarray, TimeCourse, Preprocessing
Depends: R (>= 4.4)
Imports: graphics, S4Vectors, SummarizedExperiment, methods, stats,
        utils, withr
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, GEOquery,
        tauFisher, nnet, TimeSignatR, zeitzeiger, AnnotationDbi,
        org.Mm.eg.db, org.Hs.eg.db, babelgene, callr, pkgload
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://github.com/dralperenuysal/circaTime
BugReports: https://github.com/dralperenuysal/circaTime/issues
Config/roxygen2/version: 8.0.0
RoxygenNote: 7.3.2
Config/pak/sysreqs: zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-08 09:47:43 UTC
RemoteUrl: https://github.com/BiocStaging/circaTime
RemoteRef: HEAD
RemoteSha: 4790ef8d4a85371303706cd6f2a623750e716f59
NeedsCompilation: no
Packaged: 2026-10-08 12:16:22 UTC; root
Author: Alperen Uysal [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3777-6411>)
Maintainer: Alperen Uysal <dralperenuysal@gmail.com>