{ "_id": "6a1c12ea1d7bb097a0a2f0d6", "Package": "RFGeneRank", "Title": "RFGeneRank: Cross-validated Stable Predictive Gene Ranking for\nTranscriptomics", "Version": "1.1.0", "Authors@R": "c(\nperson(\"Abdulaziz\", \"Albeshri\",\nemail = \"a.z.a1410@hotmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0718-2439\")),\nperson(\"Thamer\", \"Ahmad Bouback\",\nemail = \"Tbouback@kau.edu.sa\",\nrole = \"ctb\"),\nperson(\"Majid\", \"Al-Zahrani\",\nemail = \"maalzahrani4@kau.edu.sa\",\nrole = \"ctb\"),\nperson(\"Tasneem\", \"Alsahafi\",\nemail = \"Talsahafi0015@stu.kau.edu.sa\",\nrole = \"ctb\")\n)", "Description": "Tools to harmonize bulk RNA-seq matrices, optionally apply\nbatch correction, and train cross-validated classification\nmodels using ranger, glmnet, or xgboost. Supports leakage-safe\nfeature selection, permutation importance, SHAP-based\ninterpretability, and calibration methods (Platt or isotonic).\nProvides stability metrics across folds, embeddings (PCA/UMAP),\nROC visualization, SHAP dependence plots, and tidy ranked-gene\ntables for downstream analysis.", "License": "MIT + file LICENSE", "URL": "https://github.com/Abdulaziz-Albeshri/RFGeneRank", "BugReports": "https://github.com/Abdulaziz-Albeshri/RFGeneRank/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "biocViews": "Transcriptomics, RNASeq, GeneExpression, FeatureExtraction,\nClassification, Visualization, Software, StatisticalMethod,\nAlignment", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Collate": "'globals.R' 'class_def.R' 'accessors.R' 'accessors_public.R'\n'check_utils.R' 'batch_correct.R' 'calibrate.R'\n'combat_helpers.R' 'compute_class_weights.R' 'confounding.R'\n'crossval.R' 'id_map.R' 'plots_all.R' 'prepare_data.R'\n'align_datasets.R' 'rank_genes.R' 'top_genes.R' 'Rzzz.R'\n'package-doc.R' 'sign_importance.R' 'factor_dependence.R'\n'validate_genes.R'", "NeedsCompilation": "no", "Config/pak/sysreqs": "make libpng-dev libxml2-dev libssl-dev python3\nzlib1g-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": { "Date": "2026-05-31 10:45:12 UTC", "User": "root" }, "Author": "Abdulaziz Albeshri [aut, cre] (ORCID:\n),\nThamer Ahmad Bouback [ctb],\nMajid Al-Zahrani [ctb],\nTasneem Alsahafi [ctb]", "Maintainer": "Abdulaziz Albeshri ", "MD5sum": "ce8dd3addc77adef4b727d2c80606f05", "_user": "bioc", "_type": "src", "_file": "RFGeneRank_1.1.0.tar.gz", "_fileid": "e231e7eaf7cbe113f9d38de42f9d7fa60f367242a98d63d766793236d25c9837", "_filesize": 453918, "_sha256": "e231e7eaf7cbe113f9d38de42f9d7fa60f367242a98d63d766793236d25c9837", "_created": "2026-05-31T10:45:12.000Z", "_published": "2026-05-31T10:52:26.637Z", "_jobs": [ { "job": 78719653041, "time": 191, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7316091610" }, { "job": 78719653046, "time": 380, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7316111495" }, { "job": 78719653049, "time": 381, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7316111503" }, { "job": 78719653065, "time": 228, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7316095570" }, { "job": 78719653052, "time": 204, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7316092981" }, { "job": 78719340447, "time": 323, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7316069337" }, { "job": 78719653045, "time": 196, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7316092057" }, { "job": 78719653051, "time": 299, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7316102994" }, { "job": 78719653069, "time": 296, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7316102714" }, { "job": 78719653060, "time": 323, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7316105558" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26710350230", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/RFGeneRank", "_commit": { "id": "6ba66af81a926961ca5fe509ae40b7865bbd5ee6", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381609 }, "_maintainer": { "name": "Abdulaziz Albeshri", "email": "a.z.a1410@hotmail.com", "login": "abdulaziz-albeshri", "description": "", "uuid": 151993937, "orcid": "0000-0002-0718-2439" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "ranger", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "sva", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "umap", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "digest", "role": "Imports" }, { "package": "mgcv", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "xgboost", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "GEOquery", "role": "Suggests" }, { "package": "Biobase", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" }, { "package": "uwot", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "matrixStats", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "fastshap", "role": "Suggests" }, { "package": "caret", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-49", "n": 2 }, { "week": "2025-52", "n": 11 }, { "week": "2026-01", "n": 1 }, { "week": "2026-04", "n": 4 }, { "week": "2026-14", "n": 3 }, { "week": "2026-15", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.1.0", "bioc": "3.24" }, { "branch": "release", "version": "1.0.0", "bioc": "3.23" } ], "_topics": [ "transcriptomics", "rnaseq", "geneexpression", "featureextraction", "classification", "visualization", "software", "statisticalmethod", "alignment" ], "_stars": 0, "_contributors": [ { "user": "abdulaziz-albeshri", "count": 24, "uuid": 151993937 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 193, "source": "https://www.bioconductor.org/packages/stats/bioc/RFGeneRank" }, "_devurl": "https://github.com/abdulaziz-albeshri/rfgenerank", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/RFGeneRank.html", "manual.pdf" ], "_homeurl": "https://github.com/abdulaziz-albeshri/rfgenerank", "_realowner": "bioc", "_cranurl": false, "_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" ], "_help": [ { "page": "align_datasets", "title": "Align and merge expression + metadata (genes by intersection; strict sample match)", "topics": [ "align_datasets" ] }, { "page": "apply_calibration", "title": "Apply stored calibration to a numeric vector of probabilities", "topics": [ "apply_calibration" ] }, { "page": "calibrate_oof", "title": "Calibrate out-of-fold probabilities (isotonic or Platt)", "topics": [ "calibrate_oof" ] }, { "page": "factor_dependence", "title": "Covariate dependence of gene contributions (SHAP/proxy; \"expr\" assay)", "topics": [ "factor_dependence" ] }, { "page": "GeneRankFit-accessors", "title": "Accessors for GeneRankFit", "topics": [ "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" ] }, { "page": "id_map", "title": "Map gene identifiers using AnnotationDbi", "topics": [ "id_map" ] }, { "page": "plot_confusion_heatmap", "title": "Confusion-matrix heatmap", "topics": [ "plot_confusion_heatmap" ] }, { "page": "plot_embed", "title": "Decision-space embedding (OOF probability space): PCA or UMAP", "topics": [ "plot_embed" ] }, { "page": "plot_embed_expr", "title": "Expression-space embedding (PCA or UMAP) of top RF genes", "topics": [ "plot_embed_expr" ] }, { "page": "plot_importance", "title": "Feature importance (top genes)", "topics": [ "plot_importance" ] }, { "page": "plot_roc", "title": "ROC curve from OOF probabilities (single model)", "topics": [ "plot_roc" ] }, { "page": "plot_roc_multi", "title": "Multi-model ROC (guardrailed OOF)", "topics": [ "plot_roc_multi" ] }, { "page": "plot_shap_dependence", "title": "SHAP dependence scatter for one gene (cached-first, robust, fast)", "topics": [ "plot_shap_dependence" ] }, { "page": "plot_sign_importance", "title": "Signed feature importance (directional effect)", "topics": [ "plot_sign_importance" ] }, { "page": "prepare_data", "title": "Prepare matrices + metadata: align, (log) transform, batch correct, prefilter", "topics": [ "prepare_data" ] }, { "page": "rank_genes", "title": "Rank genes with batch-aware cross-validation (UMAP-free)", "topics": [ "rank_genes" ] }, { "page": "rfgr_crossval", "title": "Batch-aware cross-validation with optional ComBat modes (incl. frozen ComBat)", "topics": [ "rfgr_crossval" ] }, { "page": "rfgr_plot_suite", "title": "One-call plot suite (optional file export)", "topics": [ "rfgr_plot_suite" ] }, { "page": "shap_train_ranger", "title": "Compute a SHAP matrix using a single ranger model", "topics": [ "shap_train_ranger" ] }, { "page": "sign_importance", "title": "Signed feature importance for RFGeneRank models", "topics": [ "sign_importance" ] }, { "page": "top_genes", "title": "Extract top predictive genes from a GeneRankFit", "topics": [ "top_genes" ] }, { "page": "validate_genes", "title": "Validate a ranked gene set with alternate learners via k-fold CV", "topics": [ "validate_genes" ] } ], "_readme": "https://github.com/bioc/RFGeneRank/raw/HEAD/README.md", "_rundeps": [ "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" ], "_vignettes": [ { "source": "RFGeneRank.Rmd", "filename": "RFGeneRank.html", "title": "RFGeneRank: Cross-validated, stable predictive gene ranking for transcriptomics", "author": "Abdulaziz Albeshri", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "Introduction and Motivation", "Relation to existing Bioconductor packages", "Installation", "A small runnable example", "Step 1: prepare_data()", "Step 2: rank_genes()", "Step 3: downstream utilities", "Top genes", "Signed importance (directionality)", "Basic plots", "Session information" ], "created": "2025-12-28 02:53:39", "modified": "2026-03-30 21:02:27", "commits": 2 } ], "_score": 4.544068044350276, "_indexed": true, "_nocasepkg": "rfgenerank", "_universes": [ "bioc", "abdulaziz-albeshri" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-05-31T10:49:18.000Z", "distro": "noble", "commit": "6ba66af81a926961ca5fe509ae40b7865bbd5ee6", "fileid": "bc9b3517b0669d95707b397d03baa4927bf707f717a8c6fdae12adcb7caa03fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710350230" }, { "r": "4.6.0", "os": "linux", "version": "1.1.0", "date": "2026-05-31T10:49:53.000Z", "distro": "noble", "commit": "6ba66af81a926961ca5fe509ae40b7865bbd5ee6", "fileid": "6cda106880cefe2ca8513f2ac47b27f82ff6a1f259b25d677822638f465a5b04", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710350230" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-05-31T10:47:54.000Z", "commit": "6ba66af81a926961ca5fe509ae40b7865bbd5ee6", "fileid": "39dc84f8a14312f7df254aa76609eb51f150d3551dcba94325c37eaae5df733f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710350230" }, { "r": "4.6.0", "os": "mac", "version": "1.1.0", "date": "2026-05-31T10:47:26.000Z", "commit": "6ba66af81a926961ca5fe509ae40b7865bbd5ee6", "fileid": "0e245bc6f056b14a5f16e8726f99e6d3ebd300d6fc8d00484df95651d12c39aa", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710350230" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-05-31T10:49:00.000Z", "commit": "6ba66af81a926961ca5fe509ae40b7865bbd5ee6", "fileid": "5c6bba3ee899f344a58a415cdacf506867585de910d6112e348d6dcc8c405855", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710350230" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-05-31T10:47:51.000Z", "commit": "6ba66af81a926961ca5fe509ae40b7865bbd5ee6", "fileid": "1454ce548c9ecaae1446324b8f6ab5ffe30f5bff435744a3f591e62ba8058b4c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710350230" }, { "r": "4.5.3", "os": "win", "version": "1.1.0", "date": "2026-05-31T10:47:52.000Z", "commit": "6ba66af81a926961ca5fe509ae40b7865bbd5ee6", "fileid": "b6eed413ba7adaeb0f32dc374aa46adafb04422643ff4b664e659f85850d45ec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710350230" }, { "r": "4.6.0", "os": "win", "version": "1.1.0", "date": "2026-05-31T10:47:54.000Z", "commit": "6ba66af81a926961ca5fe509ae40b7865bbd5ee6", "fileid": "47be749a201a04ef6bdef41db9bc92ca95f5b103888e39bd19dde6cad9e6ea51", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710350230" } ] }