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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>.
| Version: | 0.2.3 |
| Depends: | R (≥ 4.2.0) |
| Imports: | ggplot2, stats, utils |
| Suggests: | MultiAssayExperiment, testthat (≥ 3.0.0), knitr, rmarkdown |
| Published: | 2026-09-12 |
| DOI: | 10.32614/CRAN.package.OmicsBraid |
| Author: | Adeel Farooq [aut, cre] |
| Maintainer: | Adeel Farooq <jhwanj9 at gmail.com> |
| BugReports: | https://github.com/microbes-potential/OmicsBraid/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/microbes-potential/OmicsBraid, https://microbes-potential.github.io/OmicsBraid/ |
| NeedsCompilation: | no |
| Citation: | OmicsBraid citation info |
| Materials: | README, NEWS |
| CRAN checks: | OmicsBraid results |
| Reference manual: | OmicsBraid.html , OmicsBraid.pdf |
| Package source: | OmicsBraid_0.2.3.tar.gz |
| Windows binaries: | r-devel: OmicsBraid_0.2.3.zip, r-release: OmicsBraid_0.2.3.zip, r-oldrel: OmicsBraid_0.2.3.zip |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): OmicsBraid_0.2.3.tgz, r-release (x86_64): OmicsBraid_0.2.3.tgz, r-oldrel (x86_64): OmicsBraid_0.2.3.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.