RFGeneRank
RFGeneRank: Cross-validated Stable Predictive Gene Ranking for Transcriptomics
Bioconductor version: 3.24 · Package version: 1.1.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RFGeneRank")Details
| Maintainer | Abdulaziz Albeshri <a.z.a1410@hotmail.com> |
| Author | Abdulaziz Albeshri [aut, cre] (ORCID: <https://orcid.org/0000-0002-0718-2439>), Thamer Ahmad Bouback [ctb], Majid Al-Zahrani [ctb], Tasneem Alsahafi [ctb] |
| License | MIT + file LICENSE |
| URL | https://github.com/Abdulaziz-Albeshri/RFGeneRank |
| Bug Reports | https://github.com/Abdulaziz-Albeshri/RFGeneRank/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Classification, FeatureExtraction, GeneExpression, RNASeq, Software, StatisticalMethod, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/RFGeneRank/ |
Citation
From within R, enter citation("RFGeneRank"):
Abdulaziz Albeshri. RFGeneRank: RFGeneRank: Cross-validated Stable Predictive Gene Ranking for Transcriptomics. doi:10.18129/B9.bioc.RFGeneRank, R package version 1.1.0, https://bioconductor.org/packages/RFGeneRank.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | RFGeneRank_1.1.0.tar.gz |
| Windows binary (x86_64) | RFGeneRank_1.1.0.zip |
Dependencies
Depends: R (>= 4.5.0)
Imports: ggplot2, limma, methods, pROC, ranger, stats, SummarizedExperiment, sva, AnnotationDbi, umap, scales, utils, S4Vectors, digest, mgcv, Matrix, glmnet, xgboost, patchwork
Suggests: GEOquery, Biobase, edgeR, uwot, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, DESeq2, MASS, matrixStats, BiocGenerics, fastshap, caret, testthat (>= 3.0.0), covr