# Biological Data Analysis and Visualization

## Documentation for package ‘BioUtils’ version 0.1.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

adaptive.t.test | Perform Adaptive T-Test
adjust.pvalues | Adjust P-Values for Multiple Comparisons
analyze.gene | Analyze Gene Expression Between Groups
build.analysis.df | Build Analysis Data Frame
classify.effect.size | Classify Effect Size
compute.ci | Compute Confidence Interval for Effect Size
compute.effect.size | Compute Effect Size (Cohen's d)
correlation.heatmap.plot | Plot Gene Co-expression Correlation Heatmap
extract.expression | Extract Expression and Metadata from GEO Dataset
find.probe.by.gene | Find Probe IDs by Gene Name
fit.lasso | Fit LASSO Regression for Multi-Gene Biomarker Discovery
flag.biological.relevance | Assess Biological Relevance of Gene Expression Differences
gene.analysis.plot | Plot Gene Expression with Automatic Statistical Analysis
gene.correlation.matrix | Compute Pairwise Gene Co-expression Correlation Matrix
get.gene.expression | Extract Gene Expression by Probe ID
get.gene.name | Resolve Probe IDs to Gene Names
load.geo.soft | Load GEO Dataset from SOFT File
nonparametric.test | Perform Nonparametric Group Comparison
pca.plot | Plot PCA of Sample Expression Profiles
run.gsea | Run Gene Set Enrichment Analysis
run.limma.de | Run Differential Expression Analysis Using limma
volcano.plot | Plot Volcano Plot from Differential Expression Results