Package: OmicsBraid
Type: Package
Title: Covariance-Aware Inference of Cross-Omic Effect Trajectories
Version: 0.2.2
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.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.2.0)
Imports: ggplot2, stats, utils
Suggests: MultiAssayExperiment, testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
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"))
URL: https://microbes-potential.github.io/OmicsBraid/,
        https://github.com/microbes-potential/OmicsBraid
BugReports: https://github.com/microbes-potential/OmicsBraid/issues
Repository: https://microbes-potential.r-universe.dev
Date/Publication: 2026-08-21 15:19:51 UTC
RemoteUrl: https://github.com/microbes-potential/omicsbraid
RemoteRef: HEAD
RemoteSha: 94beac15565ed774fbec9f1cb57bdaa2dc3fbe97
NeedsCompilation: no
Packaged: 2026-10-14 08:06:16 UTC; root
Author: Adeel Farooq [aut, cre]
Maintainer: Adeel Farooq <jhwanj9@gmail.com>