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