R: LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis

# LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis

## Documentation for package ‘LimROTS’ version 1.4.0

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

## Help Pages

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
Boot_parallel | Parallel processing handling function
Boot_parallel_survival | Parallel processing handling function for LimROTS survival
calculateFalseDiscoveryRate | Calculate False Discovery Rate (FDR) Using Permuted Values (Adjusted)
calOverlaps | Calculate Overlaps Between Observed and Permuted Data
calOverlaps_slr | Calculate Overlaps for Single-Label Replicates (SLR)
Check_meta_info | Check if meta info is correct
Check_SummarizedExperiment | Check if SummarizedExperiment or data is correct
countLargerThan | Count Larger Permuted Values (Modified)
fit_survival | Final Per-Feature Survival Model Fit on the Full Dataset
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
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
Optimizing | Optimize Parameters Based on Overlap Calculations
permutating_survival | Perform Per-Feature Survival Modeling on Permuted Data
SanityChecK | Sanity Check for Input Data and Parameters
UPS1.Case4 | Spectronaut and ScaffoldDIA UPS1 Spiked Dataset case 4