markeR
This is the development version of markeR; for the stable release version, see markeR.
An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
Bioconductor version: Development (3.24)
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.
Author: Rita Martins-Silva [aut, cre] 
, Alexandre Kaizeler [aut, ctb] , Nuno Luís Barbosa-Morais [aut, led, ths]
Maintainer: Rita Martins-Silva <rita.silva at gimm.pt>
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 1.3.1, https://bioconductor.org/packages/markeR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("markeR")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("markeR")| Introduction to markeR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, GeneExpression, GeneSetEnrichment, Software, Transcriptomics, Visualization |
| Version | 1.3.1 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | Artistic-2.0 |
| 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 |
| System Requirements | |
| URL | https://diseasetranscriptomicslab.github.io/markeR/ https://github.com/DiseaseTranscriptomicsLab/markeR https://doi.org/10.1093/nargab/lqag057 |
| Bug Reports | https://github.com/DiseaseTranscriptomicsLab/markeR/issues |
See More
| Suggests | devtools, markdown, renv, testthat, BiocManager, knitr, rmarkdown, roxygen2, mockery, covr, magick, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | markeR_1.3.1.tar.gz |
| Windows Binary (x86_64) | markeR_1.3.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | markeR_1.3.1.tgz |
| macOS Binary (sonoma-arm64) | markeR_1.3.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/markeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/markeR |
| Package Short Url | https://bioconductor.org/packages/markeR/ |
| Package Downloads Report | Download Stats |