In the RStudio console, cut and paste the following commands:
download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/limma-proteomics-analysis-August-2025/master/legacy-report.pg_matrix.tsv", "./legacy-report.pg_matrix.tsv")
download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/limma-proteomics-analysis-August-2025/master/Annotation_file_timsTOF.txt", "./Annotation_file_timsTOF.txt")
download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/limma-proteomics-analysis-August-2025/master/limma_proteomics_tutorial.Rmd", "./limma_proteomics_tutorial.Rmd")
download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/limma-proteomics-analysis-August-2025/master/KEGG_enrichment.Rmd", "./KEGG_enrichment.Rmd")