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).
| Version: | 0.1.3 |
| Depends: | R (≥ 3.1.2) |
| Imports: | tidyr, GEOquery, Biobase, limma, glmnet, ggplot2, pheatmap, grDevices, fgsea |
| Suggests: | knitr, rmarkdown, msigdbr, plotly |
| Published: | 2026-05-22 |
| DOI: | 10.32614/CRAN.package.BioUtils (may not be active yet) |
| Author: | Spencer Treadway [aut, cre] |
| Maintainer: | Spencer Treadway <spencer.treadway08 at gmail.com> |
| License: | MIT + file LICENSE |
| URL: | https://spencertreadway.github.io/BioUtils/, https://github.com/spencertreadway/BioUtils |
| NeedsCompilation: | no |
| Materials: | README, NEWS |
| CRAN checks: | BioUtils results |
| Reference manual: | BioUtils.html , BioUtils.pdf |
| Vignettes: |
BioUtils: A Case Study in Transcriptomic Analysis of Renal Cell Carcinoma (source, R code) Transcriptomic Signatures of Renal Cell Carcinoma (source, R code) |
| Package source: | BioUtils_0.1.3.tar.gz |
| Windows binaries: | r-devel: not available, r-release: BioUtils_0.1.3.zip, r-oldrel: not available |
| macOS binaries: | r-release (arm64): BioUtils_0.1.3.tgz, r-oldrel (arm64): BioUtils_0.1.3.tgz, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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