Bioconductor release scheduled for October 29

markeR

This is the development version of markeR; to use it, please install the devel version of Bioconductor.

An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers


Bioconductor version: Development (3.22)

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] ORCID iD ORCID: 0000-0002-1067-7993 , Alexandre Kaizeler [aut, ctb] ORCID iD ORCID: 0000-0002-9117-6073 , Nuno Luís Barbosa-Morais [aut, led, ths] ORCID iD ORCID: 0000-0002-1215-0538

Maintainer: Rita Martins-Silva <rita.silva at medicina.ulisboa.pt>

Citation (from within R, enter citation("markeR")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 PDF
NEWS Text

Details

biocViews Classification, GeneExpression, GeneSetEnrichment, Software, Transcriptomics, Visualization
Version 0.99.6
In Bioconductor since BioC 3.22 (R-4.5)
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
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
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package markeR_0.99.6.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64) markeR_0.99.6.tgz
macOS Binary (arm64) markeR_0.99.6.tgz
Source Repository git clone https://git.bioconductor.org/packages/markeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/markeR
Bioc Package Browser https://code.bioconductor.org/browse/markeR/
Package Short Url https://bioconductor.org/packages/markeR/
Package Downloads Report Download Stats