Bootstrap Prediction Uncertainty and Its Biological Drivers in Gene-Expression Models

Fits bootstrap ensembles of penalized regression models on bulk gene-expression data, derives per-sample uncertainty scores from out-of-bag predictions, and tests whether technical covariates explain that uncertainty. The bootstrap method is described by Efron and Tibshirani (1993, ISBN:9780412042317), and elastic-net regression follows Friedman, Hastie, and Tibshirani (2010) . The optional immunedeconv package, used for immune-cell deconvolution, is available from GitHub < https://github.com/omnideconv/immunedeconv>.