Package index • LimROTS

All functions
`Boot_parallel()`	Parallel processing handling function
`Boot_parallel_survival()`	Parallel processing handling function for LimROTS survival
`Check_SummarizedExperiment()`	Check if SummarizedExperiment or data is correct
`Check_meta_info()`	Check if meta info is correct
`LimROTS()`	`LimROTS`: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis
`LimROTS_survival()`	`LimROTS_survival`: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust survival analysis in Omics Data
`Limma_bootstrap()`	Perform Linear Modeling with Covariates using Limma
`Limma_fit()`	Perform Linear Modeling with Covariates using Limma
`Limma_permutating()`	Perform Permutation-Based Linear Modeling with Covariates using Limma
`Optimizing()`	Optimize Parameters Based on Overlap Calculations
`SanityChecK()`	Sanity Check for Input Data and Parameters
`UPS1.Case4`	Spectronaut and ScaffoldDIA UPS1 Spiked Dataset case 4
`bootstrapS()`	Generate Bootstrap Samples
`bootstrapSamples_limRots()`	Generate Stratified Bootstrap Samples for limRots
`bootstrapSamples_limRots_block()`	Generate Stratified Bootstrap Samples with Correlation Blocks
`bootstrapSamples_limRots_cox()`	Generate Stratified Bootstrap Samples for Cox limRots with Correlation Blocks
`bootstrap_survival()`	Perform Per-Feature Survival Modeling on Bootstrap Resamples
`calOverlaps()`	Calculate Overlaps Between Observed and Permuted Data
`calOverlaps_slr()`	Calculate Overlaps for Single-Label Replicates (SLR)
`calculateFalseDiscoveryRate()`	Calculate False Discovery Rate (FDR) Using Permuted Values (Adjusted)
`countLargerThan()`	Count Larger Permuted Values (Modified)
`fit_survival()`	Final Per-Feature Survival Model Fit on the Full Dataset
`permutating_survival()`	Perform Per-Feature Survival Modeling on Permuted Data

Reference

All functions