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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: BioUtils_0.1.3.zip |
| 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 |
Please use the canonical form https://CRAN.R-project.org/package=BioUtils to link to this page.
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.
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