Package: OmicsBraid
Type: Package
Title: Covariance-Aware Inference of Cross-Omic Effect Trajectories
Description: A research-oriented statistical framework for comparing standardized
    biological effects across matched omics layers. It estimates layer-specific
    standardized effects, accounts for cross-omic dependence using matched-subject
    bootstrap correlations, tests multivariate omnibus evidence, synthesizes
    consensus effects with generalized least squares, quantifies cross-omic
    heterogeneity, performs practical-equivalence testing, fits covariance-aware
    ordered GLS effect trajectories, classifies hierarchical cross-layer effect
    patterns with separate confirmatory and suggestive states, supports analytic
    and subject-bootstrap confidence intervals for layer and consensus effects,
    supports empirical matched-subject permutation and centered-bootstrap
    calibration of omnibus and heterogeneity tests for non-Gaussian settings,
    and creates evidence-forest and effect-braid visualizations. The package is
    designed for analysis-ready bulk multi-omics data or externally estimated
    summary statistics. It does not perform raw sequencing or mass-spectrometry
    preprocessing. Methodological components draw on standardized mean-difference 
    estimation described by Hedges (1981) <doi:10.3102/10769986006002107>,
    bootstrap resampling described by Efron (1979)
    <doi:10.1214/aos/1176344552>, and two one-sided equivalence testing
    described by Schuirmann (1987) <doi:10.1007/BF01068419>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.2.0)
Imports: ggplot2, stats, utils
Suggests: MultiAssayExperiment, testthat (>= 3.0.0), knitr, rmarkdown
Config/testthat/edition: 3
Config/Needs/website: pkgdown
Config/roxygen2/version: 8.1.0
Authors@R: person("Adeel", "Farooq", email = "jhwanj9@gmail.com", role = c("aut", "cre"))
Version: 0.2.3
URL: https://github.com/microbes-potential/OmicsBraid,
        https://microbes-potential.github.io/OmicsBraid/
BugReports: https://github.com/microbes-potential/OmicsBraid/issues
NeedsCompilation: no
Packaged: 2026-09-01 17:03:31 UTC; mahad
Author: Adeel Farooq [aut, cre]
Maintainer: Adeel Farooq <jhwanj9@gmail.com>
Repository: CRAN
Date/Publication: 2026-09-12 09:30:02 UTC
