markeR
An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
Bioconductor version: 3.23 · Package version: 1.2.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
markeR is an R package that provides a modular and extensible framework for the systematic evaluation of gene sets as phenotypic markers using transcriptomic data. The package is designed to support both quantitative analyses and visual exploration of gene set behaviour across experimental and clinical phenotypes. It implements multiple methods, including score-based and enrichment approaches, and also allows the exploration of expression behaviour of individual genes. In addition, users can assess the similarity of their own gene sets against established collections (e.g., those from MSigDB), facilitating biological interpretation.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("markeR")Details
| Maintainer | Rita Martins-Silva <rita.silva@medicina.ulisboa.pt> |
| Author | Rita Martins-Silva [aut, cre] (ORCID: <https://orcid.org/0000-0002-1067-7993>), Alexandre Kaizeler [aut, ctb] (ORCID: <https://orcid.org/0000-0002-9117-6073>), Nuno Luís Barbosa-Morais [aut, led, ths] (ORCID: <https://orcid.org/0000-0002-1215-0538>) |
| License | Artistic-2.0 |
| URL | https://diseasetranscriptomicslab.github.io/markeR/, https://github.com/DiseaseTranscriptomicsLab/markeR |
| Bug Reports | https://github.com/DiseaseTranscriptomicsLab/markeR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, GeneExpression, GeneSetEnrichment, Software, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/markeR/ |
Citation
From within R, enter citation("markeR"):
Rita Martins-Silva, Alexandre Kaizeler, Nuno Luís Barbosa-Morais. markeR: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers. doi:10.18129/B9.bioc.markeR, R package version 1.2.0, https://bioconductor.org/packages/markeR.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | markeR_1.2.0.tar.gz |
| Windows binary (x86_64) | markeR_1.2.0.zip |
| macOS binary (arm64) | markeR_1.2.0.tgz |
| macOS binary (x86_64) | markeR_1.2.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: circlize, edgeR, ComplexHeatmap, ggh4x, ggplot2, ggpubr, grid, gridExtra, pROC, RColorBrewer, reshape2, rstatix, scales, stats, utils, fgsea, limma, ggrepel, effectsize, msigdbr, tibble
Suggests: devtools, markdown, renv, testthat, BiocManager, knitr, rmarkdown, roxygen2, mockery, covr, magick, BiocStyle