Main

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: markeR
 Title: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
-Version: 1.2
+Version: 1.3.1
 Authors@R: 
     c(
       person("Rita", "Martins-Silva", 
-             email = "rita.silva@medicina.ulisboa.pt", 
+             email = "rita.silva@gimm.pt", 
              role = c("aut", "cre"),
              comment = c(ORCID = "0000-0002-1067-7993")), 
             person("Alexandre", "Kaizeler",  
@@ -66,7 +66,8 @@ Config/testthat/edition: 3
 Depends: 
     R (>= 4.5.0)
 URL: https://diseasetranscriptomicslab.github.io/markeR/,
-     https://github.com/DiseaseTranscriptomicsLab/markeR
+     https://github.com/DiseaseTranscriptomicsLab/markeR,
+     https://doi.org/10.1093/nargab/lqag057 
 BugReports: https://github.com/DiseaseTranscriptomicsLab/markeR/issues
 VignetteBuilder: knitr
 Config/Needs/website: rmarkdown

NEWS.md

@@ -1,3 +1,14 @@
+# markeR 1.3.1 (8 Jul 2026)
+
+## Minor Changes
+- Updated the citation to the markeR paper published in NAR Genomics and Bioinformatics.
+- Updated the contact email address.
+- Fixed `runGSEA` function.
+
+# markeR 1.2 (29 Apr, 2026) 
+
+- Bioconductor Release 3.23
+
 # markeR 1.1.2 (12 Mar, 2026) 
 
 ## Minor Changes

R/runGSEA.R

@@ -162,7 +162,13 @@ runGSEA <- function(DEGList, gene_sets, stat = NULL, ContrastCorrection=FALSE, n
     list_of_dfs <- split(combined_df, combined_df$df_name)
 
     # Step 4: Remove the helper column
-    list_of_dfs <- lapply(list_of_dfs, function(df) df[, !names(df) %in% "df_name"])
+    #list_of_dfs <- lapply(list_of_dfs, function(df) df[, !names(df) %in% "df_name"])
+
+    list_of_dfs <- lapply(list_of_dfs, function(df) {
+      df$df_name <- NULL
+      df
+    })
+
     results_by_contrast <- list_of_dfs[names(results_by_contrast)]
 
   } else {

README.Rmd

@@ -30,7 +30,8 @@ knitr::opts_chunk$set(
 
 > **To cite `markeR` please use:** 
 >
-> Martins-Silva R, Kaizeler A, Barbosa-Morais NL (2025). _markeR: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers_. doi:10.18129/B9.bioc.markeR, R package version 1.2, https://bioconductor.org/packages/markeR.
+> Martins-Silva R, Kaizeler A, Barbosa-Morais NL (2026). "Exploring molecular signatures of senescence with markeR, an R Toolkit for evaluating gene sets as
+  phenotypic markers." NAR Genomics and Bioinformatics, 8(2), lqag057. doi:10.1093/nargab/lqag057
 
 The folder `inst/Paper/` is in the **paper** branch and contains all scripts and materials used in the original `markeR` paper to reproduce analyses and figures.  You can browse it [here](https://github.com/DiseaseTranscriptomicsLab/markeR/tree/paper/inst/Paper).
 

README.md

@@ -24,10 +24,10 @@ across experimental and clinical phenotypes.
 
 > **To cite `markeR` please use:**
 >
-> Martins-Silva R, Kaizeler A, Barbosa-Morais NL (2025). *markeR: An R
-> Toolkit for Evaluating Gene Signatures as Phenotypic Markers*.
-> <doi:10.18129/B9.bioc.markeR>, R package version 1.2,
-> <https://bioconductor.org/packages/markeR>.
+> Martins-Silva R, Kaizeler A, Barbosa-Morais NL (2026). “Exploring
+> molecular signatures of senescence with markeR, an R Toolkit for
+> evaluating gene sets as phenotypic markers.” NAR Genomics and
+> Bioinformatics, 8(2), lqag057. <doi:10.1093/nargab/lqag057>
 
 The folder `inst/Paper/` is in the **paper** branch and contains all
 scripts and materials used in the original `markeR` paper to reproduce

inst/CITATION

@@ -0,0 +1,25 @@
+citHeader("To cite markeR in publications use:")
+
+bibentry(
+  bibtype = "Article",
+  title = "Exploring molecular signatures of senescence with markeR, an R Toolkit for evaluating gene sets as phenotypic markers",
+  author = c(
+    person("Rita", "Martins-Silva"),
+    person("Alexandre", "Kaizeler"),
+    person("Nuno L", "Barbosa-Morais")
+  ),
+  journal = "NAR Genomics and Bioinformatics",
+  volume = "8",
+  number = "2",
+  pages = "lqag057",
+  year = "2026",
+  doi = "10.1093/nargab/lqag057",
+  textVersion =
+    paste(
+      "Martins-Silva R, Kaizeler A, Barbosa-Morais NL (2026).",
+      "\"Exploring molecular signatures of senescence with markeR,",
+      "an R Toolkit for evaluating gene sets as phenotypic markers.\"",
+      "NAR Genomics and Bioinformatics, 8(2), lqag057.",
+      "doi:10.1093/nargab/lqag057"
+    )
+)