RFGeneRank
This is the development version of RFGeneRank; to use it, please install the devel version of Bioconductor.
RFGeneRank: Cross-validated Stable Predictive Gene Ranking for Transcriptomics
Bioconductor version: Development (3.23)
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.
Author: Abdulaziz Albeshri [aut, cre]
, Thamer Ahmad Bouback [ctb], Majid Al-Zahrani [ctb], Tasneem Alsahafi [ctb]
Maintainer: Abdulaziz Albeshri <a.z.a1410 at hotmail.com>
citation("RFGeneRank")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("RFGeneRank")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RFGeneRank")| RFGeneRank | HTML | R Script |
| Reference Manual |
Details
| biocViews | Alignment, Classification, FeatureExtraction, GeneExpression, RNASeq, Software, StatisticalMethod, Transcriptomics, Visualization |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | ggplot2, limma, methods, pROC, ranger, stats, SummarizedExperiment, sva, AnnotationDbi, umap, scales, utils, S4Vectors, digest, mgcv, Matrix, glmnet, xgboost, patchwork |
| System Requirements | |
| URL | https://github.com/Abdulaziz-Albeshri/RFGeneRank |
| Bug Reports | https://github.com/Abdulaziz-Albeshri/RFGeneRank/issues |
See More
| Suggests | GEOquery, Biobase, edgeR, uwot, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, DESeq2, MASS, matrixStats, BiocGenerics, fastshap, caret, testthat (>= 3.0.0), covr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RFGeneRank_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/RFGeneRank |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RFGeneRank |
| Bioc Package Browser | https://code.bioconductor.org/browse/RFGeneRank/ |
| Package Short Url | https://bioconductor.org/packages/RFGeneRank/ |
| Package Downloads Report | Download Stats |