Covariance-Aware Inference of Cross-Omic Effect Trajectories R package OmicsBraid version 0.2.3 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>. Software Depends: R (>= 4.2.0) Imports: ggplot2, stats, utils Suggests: MultiAssayExperiment, testthat (>= 3.0.0), knitr, rmarkdown Adeel Farooq <jhwanj9@gmail.com> Comprehensive R Archive Network (CRAN) Adeel Farooq [aut, cre] MIT + file LICENSE (https://CRAN.R-project.org/package=OmicsBraid/LICENSE) 2026-09-12 application/tgz https://CRAN.R-project.org/package=OmicsBraid doi:10.32614/CRAN.package.OmicsBraid