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OmicsBraid  

Covariance-Aware Inference of Cross-Omic Effect Trajectories
View on CRAN: Click here


Download and install OmicsBraid package within the R console
Install from CRAN:
install.packages("OmicsBraid")

Install from Github:
library("remotes")
install_github("cran/OmicsBraid")

Install by package version:
library("remotes")
install_version("OmicsBraid", "0.2.3")



Attach the package and use:
library("OmicsBraid")
Maintained by
Adeel Farooq
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-09-12
Latest Update: 2026-09-12
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>.
How to cite:
Adeel Farooq (2026). OmicsBraid: Covariance-Aware Inference of Cross-Omic Effect Trajectories. R package version 0.2.3, https://cran.r-project.org/web/packages/OmicsBraid. Accessed 03 Oct. 2026.
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