Package: BioUtils
Title: Biological Data Analysis and Visualization
Version: 0.1.3
Authors@R: 
    person("Spencer", "Treadway", , "spencer.treadway08@gmail.com", role = c("aut", "cre"))
Description: 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).
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.1.2)
Suggests: knitr, rmarkdown, msigdbr, plotly
VignetteBuilder: knitr
Imports: tidyr, GEOquery, Biobase, limma, glmnet, ggplot2, pheatmap,
        grDevices, fgsea
URL: https://spencertreadway.github.io/BioUtils/,
        https://github.com/spencertreadway/BioUtils
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-05-18 23:18:01 UTC; spenc
Author: Spencer Treadway [aut, cre]
Maintainer: Spencer Treadway <spencer.treadway08@gmail.com>
Repository: CRAN
Date/Publication: 2026-05-22 20:24:09 UTC
Built: R 4.5.3; ; 2026-05-23 15:22:38 UTC; windows
