RFGeneRank
This is the released version of RFGeneRank; for the devel version, see RFGeneRank.
RFGeneRank: Cross-validated Stable Predictive Gene Ranking for Transcriptomics
Bioconductor version: Release (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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Classification, FeatureExtraction, GeneExpression, RNASeq, Software, StatisticalMethod, Transcriptomics, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | RFGeneRank_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | |
| 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 |