Package index
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Boot_parallel() - Parallel processing handling function
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Check_SummarizedExperiment() - Check if SummarizedExperiment or data is correct
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Check_meta_info() - Check if meta info is correct
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LimROTS() LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Analysis of Proteomics and Metabolomics Data
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Limma_bootstrap() - Perform Linear Modeling with Covariates using Limma
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Limma_fit() - Perform Linear Modeling with Covariates using Limma
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Limma_permutating() - Perform Permutation-Based Linear Modeling with Covariates using Limma
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Optimizing() - Optimize Parameters Based on Overlap Calculations
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SanityChecK() - Sanity Check for Input Data and Parameters
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UPS1.Case4 - Spectronaut and ScaffoldDIA UPS1 Spiked Dataset case 4
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bootstrapS() - Generate Bootstrap Samples
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bootstrapSamples.limRots() - Generate Stratified Bootstrap Samples for limRots
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calOverlaps() - Calculate Overlaps Between Observed and Permuted Data
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calOverlaps.slr() - Calculate Overlaps for Single-Label Replicates (SLR)
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calculateFalseDiscoveryRate() - Calculate False Discovery Rate (FDR) Using Permuted Values (Adjusted)
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countLargerThan() - Count Larger Permuted Values (Modified)