RFGeneRank

RFGeneRank: Cross-validated Stable Predictive Gene Ranking for Transcriptomics

Bioconductor version: 3.23 · Package version: 1.0.0

Tools to harmonize bulk RNA-seq matrices, optionally apply batch correction, and train cross-validated classification models using ranger, glmnet, or xgboost. Supports leakage-safe feature selection, permutation importance, SHAP-based interpretability, and calibration methods (Platt or isotonic). Provides stability metrics across folds, embeddings (PCA/UMAP), ROC visualization, SHAP dependence plots, and tidy ranked-gene tables for downstream analysis.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RFGeneRank")