RTOOLS

Some useful scripts and templates I use

General Scripts

• general_functions.R: General functions
• plotting_functions.R: Functions for plotting (mainly ggplot2)
• stats_functions.R: Functions for statistics and survival analysis
• utils.R: Utility functions

Omics Scripts

• deseq_helper_functions.R: Functions for DESeq2 analysis (deprecated)
• filtering_functions.R: Functions for filtering rna-seq data
• rna_functions.R: Functions for RNA analysis
• enrichment_functions.R: Functions for enrichment analysis
• proteomics_functions.R: Functions for proteomics analysis (targeted proteomics)
• wgcna_scripts.R: Functions for WGCNA analysis
• converting_functions.R: Functions for converting data and annotations
• signature_functions.R: Functions for -omics signature analysis

Miscellaneous

• mgc*.R: Functions from Macintosh Cornwell PhD
• summarize_table_function.R: Function for summarizing tables
• clustering_functions.R: Functions for clustering analysis
• dimension_reduction_functions.R: Functions for dimension reduction analysis

Pipeline Scripts (deprecated)

• gene_ratio_functions.R: Functions for gene ratio analysis
• functional_pipelines.R: Functional pipelines