Package: RFGeneRank 1.1.0

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_1.1.0.tar.gz
RFGeneRank_1.1.0.zip(r-4.7)RFGeneRank_1.1.0.zip(r-4.6)RFGeneRank_1.1.0.zip(r-4.5)
RFGeneRank_1.1.0.tgz(r-4.6-any)RFGeneRank_1.1.0.tgz(r-4.5-any)
RFGeneRank_1.1.0.tar.gz(r-4.7-any)RFGeneRank_1.1.0.tar.gz(r-4.6-any)
RFGeneRank_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RFGeneRank/json (API)

# Install 'RFGeneRank' in R:

install.packages('RFGeneRank', repos = c('https://bioc.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)

transcriptomics rnaseq geneexpression featureextraction classification visualization software statisticalmethod alignment

4.54 score 2 scripts 27 exports 94 dependencies

Last updated from:6ba66af81a. Checks:1 NOTE, 7 OK, 2 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	243
linux-devel-x86_64	OK	390
source / vignettes	OK	333
linux-release-x86_64	OK	373
macos-release-arm64	ERROR	204
macos-oldrel-arm64	ERROR	187
windows-devel	OK	287
windows-release	OK	297
windows-oldrel	OK	312
wasm-release	OK	227

Exports:align_datasets apply_calibration calibrate_oof calibration calibration<-factor_dependence id_map imp imp<-oof params plot_confusion_heatmap plot_embed plot_embed_expr plot_importance plot_roc plot_roc_multi plot_shap_dependence plot_sign_importance prepare_data rank_genes rfgr_crossval rfgr_plot_suite shap_train_ranger sign_importance top_genes validate_genes

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl data.table DBI DelayedArray digest edgeR farver fastmap foreach formatR futile.logger futile.options genefilter generics GenomicRanges ggplot2 glmnet glue gtable here httr IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl patchwork pkgconfig png pROC R6 ranger rappdirs RColorBrewer Rcpp RcppEigen RcppTOML reticulate rlang rprojroot RSpectra RSQLite S4Arrays S4Vectors S7 scales Seqinfo shape snow SparseArray statmod SummarizedExperiment survival sva sys umap vctrs viridisLite withr xgboost XML xtable XVector

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

Rendered fromRFGeneRank.Rmdusingknitr::rmarkdown

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

Help page	Topics
Align and merge expression + metadata (genes by intersection; strict sample match)	align_datasets
Apply stored calibration to a numeric vector of probabilities	apply_calibration
Calibrate out-of-fold probabilities (isotonic or Platt)	calibrate_oof
Covariate dependence of gene contributions (SHAP/proxy; "expr" assay)	factor_dependence
Accessors for GeneRankFit	calibration 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 AnnotationDbi	id_map
Confusion-matrix heatmap	plot_confusion_heatmap
Decision-space embedding (OOF probability space): PCA or UMAP	plot_embed
Expression-space embedding (PCA or UMAP) of top RF genes	plot_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, prefilter	prepare_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 model	shap_train_ranger
Signed feature importance for RFGeneRank models	sign_importance
Extract top predictive genes from a GeneRankFit	top_genes
Validate a ranked gene set with alternate learners via k-fold CV	validate_genes

Package: RFGeneRank 1.1.0

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

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)