Analysis scripts and processed data tables for comparative proteomics of rubber tree (Hevea brasiliensis) latex across growth stages and four clones

R scripts and processed data tables for differential abundance analysis (limma) and weighted gene co-expression network analysis (WGCNA) used in the study 'Comparative proteomics of rubber tree (Hevea brasiliensis) latex across 10- and 20-year-old trees in four clones (BPM24, GT1, PB260, and RRIC100)'. This deposit includes: (1) R analysis scripts; (2) the complete quantile-normalised proteome quantification matrix; (3) differentially abundant protein lists for the global and four clone-specific comparisons; and (4) WGCNA co-expression module protein lists. Raw mass spectrometry data are available at PRIDE (PXD073738).