This repository contains source code and data files for the following paper: "Non-canonical Metabolic and Molecular Effects of Calorie Restriction Are Revealed by Varying Temporal Conditions."
The folder "Source Data" contains all the data required to recreate the volcano plots for the metabolomics/proteomics data.
R scripts for cleaning/normalizing the datasets, analyzing the data, and creating figures are included in the ("R Code") folder:
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The script "Met_Data_Cleaning_Pak_2023.R" contains code used to clean and normalize the metabolomics data.
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The script "Pro_Data_Cleaning_Pak_2023.R" contains code used to clean and normalize the proteomics data.
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The script "Met_T_Tests_Fold_Changes_Pak_2023.R" contains code used to run t-tests and fold-change analyses for the volcano plots for the metabolomics data.
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The script "Pro_T_Tests_Fold_Changes_Pak_2023.R" contains code used to run t-tests and fold-change analyses for the volcano plots for the proteomics data.
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The script "Met_PCA_Pak_2023.R" contains code used to run PCA analyses for the metabolomics data.
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The script "Pro_PCA_Pak_2023.R" contains code used to run PCA analyses for the proteomics data.
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The script "Met_MSEA_Pak_2024.R" contains code used to run metabolite set enrichment analysis.