Package: RFGeneRank
Title: RFGeneRank: Cross-validated Stable Predictive Gene Ranking for
        Transcriptomics
Version: 1.1.0
Authors@R: c(
    person("Abdulaziz", "Albeshri",
           email = "a.z.a1410@hotmail.com",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0718-2439")),
    person("Thamer", "Ahmad Bouback",
           email = "Tbouback@kau.edu.sa",
           role = "ctb"),    
    person("Majid", "Al-Zahrani",
           email = "maalzahrani4@kau.edu.sa",
           role = "ctb"),
    person("Tasneem", "Alsahafi",
           email = "Talsahafi0015@stu.kau.edu.sa",
           role = "ctb")
 )
Description: 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.
License: MIT + file LICENSE
URL: https://github.com/Abdulaziz-Albeshri/RFGeneRank
BugReports: https://github.com/Abdulaziz-Albeshri/RFGeneRank/issues
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
Config/testthat/edition: 3
VignetteBuilder: knitr
biocViews: Transcriptomics, RNASeq, GeneExpression, FeatureExtraction,
        Classification, Visualization, Software, StatisticalMethod,
        Alignment
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Collate: 'globals.R' 'class_def.R' 'accessors.R' 'accessors_public.R'
        'check_utils.R' 'batch_correct.R' 'calibrate.R'
        'combat_helpers.R' 'compute_class_weights.R' 'confounding.R'
        'crossval.R' 'id_map.R' 'plots_all.R' 'prepare_data.R'
        'align_datasets.R' 'rank_genes.R' 'top_genes.R' 'Rzzz.R'
        'package-doc.R' 'sign_importance.R' 'factor_dependence.R'
        'validate_genes.R'
NeedsCompilation: no
Config/pak/sysreqs: make libpng-dev libxml2-dev libssl-dev python3
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:06:49 UTC
RemoteUrl: https://github.com/bioc/RFGeneRank
RemoteRef: HEAD
RemoteSha: 6ba66af81a926961ca5fe509ae40b7865bbd5ee6
Packaged: 2026-07-04 21:01:20 UTC; root
Author: Abdulaziz Albeshri [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0718-2439>),
  Thamer Ahmad Bouback [ctb],
  Majid Al-Zahrani [ctb],
  Tasneem Alsahafi [ctb]
Maintainer: Abdulaziz Albeshri <a.z.a1410@hotmail.com>