Package index • BioUtils

All functions

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