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cff-version: 1.2.0
message: 'To cite package "markeR" in publications use:'
type: software
license: Artistic-2.0
title: 'markeR: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers'
version: 1.3.0
doi: 10.32614/CRAN.package.markeR
abstract: 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.
authors:
- family-names: Martins-Silva
  given-names: Rita
  email: rita.silva@medicina.ulisboa.pt
  orcid: https://orcid.org/0000-0002-1067-7993
- family-names: Kaizeler
  given-names: Alexandre
  orcid: https://orcid.org/0000-0002-9117-6073
- family-names: Barbosa-Morais
  given-names: Nuno Luís
  orcid: https://orcid.org/0000-0002-1215-0538
repository: https://bioc.r-universe.dev
repository-code: https://github.com/DiseaseTranscriptomicsLab/markeR
commit: ec844f3429bbab9ed6ea5885b1816ce71f1199a5
url: https://diseasetranscriptomicslab.github.io/markeR/
date-released: '2026-04-28'
contact:
- family-names: Martins-Silva
  given-names: Rita
  email: rita.silva@medicina.ulisboa.pt
  orcid: https://orcid.org/0000-0002-1067-7993