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

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Documentation for package ‘LimROTS’ version 1.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

bootstrapS	Generate Bootstrap Samples
bootstrapSamples_limRots	Generate Stratified Bootstrap Samples for limRots
Boot_parallel	Parallel processing handling function
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)
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
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