Biological Data Analysis and Visualization R package BioUtils version 0.1.3 Provides tools for the analysis and visualization of gene expression data from the NCBI Gene Expression Omnibus (GEO). Implements a complete workflow including data import, quality control, differential expression analysis, co-expression network analysis, pathway enrichment, and multi-gene biomarker discovery. Differential expression uses the empirical Bayes moderated t-statistic of Smyth (2004) <doi:10.2202/1544-6115.1027>. Gene set enrichment analysis follows Subramanian et al. (2005) <doi:10.1073/pnas.0506580102>. Multi-gene biomarker selection uses the LASSO method of Tibshirani (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>. Effect sizes are computed as Cohen's d following Cohen (1988). Software Depends: R (>= 3.1.2) Imports: tidyr, GEOquery, Biobase, limma, glmnet, ggplot2, pheatmap, grDevices, fgsea Suggests: knitr, rmarkdown, msigdbr, plotly Spencer Treadway <spencer.treadway08@gmail.com> Comprehensive R Archive Network (CRAN) Spencer Treadway [aut, cre] MIT + file LICENSE (https://CRAN.R-project.org/package=BioUtils/LICENSE) 2026-05-22 application/tgz https://CRAN.R-project.org/package=BioUtils doi:10.32614/CRAN.package.BioUtils