Package: RFGeneRank 1.0.0

Abdulaziz Albeshri

RFGeneRank: RFGeneRank: Cross-validated Stable Predictive Gene Ranking for Transcriptomics

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.

Authors:Abdulaziz Albeshri [aut, cre], Thamer Ahmad Bouback [ctb], Majid Al-Zahrani [ctb], Tasneem Alsahafi [ctb]

RFGeneRank_1.0.0.tar.gz
RFGeneRank_1.0.0.zip(r-4.7)RFGeneRank_1.0.0.zip(r-4.6)RFGeneRank_1.0.0.zip(r-4.5)
RFGeneRank_1.0.0.tgz(r-4.6-any)RFGeneRank_1.0.0.tgz(r-4.5-any)
RFGeneRank_1.0.0.tar.gz(r-4.7-any)RFGeneRank_1.0.0.tar.gz(r-4.6-any)
RFGeneRank_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RFGeneRank/json (API)
NEWS

# Install 'RFGeneRank' in R:
install.packages('RFGeneRank', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/abdulaziz-albeshri/rfgenerank/issues

On BioConductor:RFGeneRank-1.1.0(bioc 3.24)RFGeneRank-1.0.0(bioc 3.23)

transcriptomicsrnaseqgeneexpressionfeatureextractionclassificationvisualizationsoftwarestatisticalmethodalignment

4.54 score 188 downloads 27 exports 94 dependencies

Last updated from:9a749d081c (on RELEASE_3_23). Checks:1 NOTE, 7 OK, 2 ERROR. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE227
linux-devel-x86_64OK368
source / vignettesOK315
linux-release-x86_64OK403
macos-release-arm64ERROR203
macos-oldrel-arm64ERROR197
windows-develOK298
windows-releaseOK260
windows-oldrelOK280
wasm-releaseOK191

Exports:align_datasetsapply_calibrationcalibrate_oofcalibrationcalibration<-factor_dependenceid_mapimpimp<-oofparamsplot_confusion_heatmapplot_embedplot_embed_exprplot_importanceplot_rocplot_roc_multiplot_shap_dependenceplot_sign_importanceprepare_datarank_genesrfgr_crossvalrfgr_plot_suiteshap_train_rangersign_importancetop_genesvalidate_genes

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydigestedgeRfarverfastmapforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomicRangesggplot2glmnetgluegtableherehttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpatchworkpkgconfigpngpROCR6rangerrappdirsRColorBrewerRcppRcppEigenRcppTOMLreticulaterlangrprojrootRSpectraRSQLiteS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraystatmodSummarizedExperimentsurvivalsvasysumapvctrsviridisLitewithrxgboostXMLxtableXVector

RFGeneRank: Cross-validated, stable predictive gene ranking for transcriptomics

Abdulaziz Albeshri

Rendered fromRFGeneRank.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-30
Started: 2025-12-28

Readme and manuals

Help Manual

Help pageTopics
Align and merge expression + metadata (genes by intersection; strict sample match)align_datasets
Apply stored calibration to a numeric vector of probabilitiesapply_calibration
Calibrate out-of-fold probabilities (isotonic or Platt)calibrate_oof
Covariate dependence of gene contributions (SHAP/proxy; "expr" assay)factor_dependence
Accessors for GeneRankFitcalibration calibration,GeneRankFit-method calibration<- calibration<-,GeneRankFit-method GeneRankFit-accessors imp imp,GeneRankFit-method imp<- imp<-,GeneRankFit-method oof oof,GeneRankFit-method params params,GeneRankFit-method
Map gene identifiers using AnnotationDbiid_map
Confusion-matrix heatmapplot_confusion_heatmap
Decision-space embedding (OOF probability space): PCA or UMAPplot_embed
Expression-space embedding (PCA or UMAP) of top RF genesplot_embed_expr
Feature importance (top genes)plot_importance
ROC curve from OOF probabilities (single model)plot_roc
Multi-model ROC (guardrailed OOF)plot_roc_multi
SHAP dependence scatter for one gene (cached-first, robust, fast)plot_shap_dependence
Signed feature importance (directional effect)plot_sign_importance
Prepare matrices + metadata: align, (log) transform, batch correct, prefilterprepare_data
Rank genes with batch-aware cross-validation (UMAP-free)rank_genes
Batch-aware cross-validation with optional ComBat modes (incl. frozen ComBat)rfgr_crossval
One-call plot suite (optional file export)rfgr_plot_suite
Compute a SHAP matrix using a single ranger modelshap_train_ranger
Signed feature importance for RFGeneRank modelssign_importance
Extract top predictive genes from a GeneRankFittop_genes
Validate a ranked gene set with alternate learners via k-fold CVvalidate_genes