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
