From 561b8d7c70e979ab113d64304067815df28877a7 Mon Sep 17 00:00:00 2001 From: Rita Silva Date: Fri, 8 May 2026 15:41:02 +0100 Subject: [PATCH 1/4] dev v1.3 --- DESCRIPTION | 2 +- README.Rmd | 2 +- README.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index aab1bbb1..f9c30584 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: markeR Title: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers -Version: 1.2 +Version: 1.3 Authors@R: c( person("Rita", "Martins-Silva", diff --git a/README.Rmd b/README.Rmd index 4bfc4ca5..da4d6b38 100644 --- a/README.Rmd +++ b/README.Rmd @@ -30,7 +30,7 @@ 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 (2025). _markeR: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers_. doi:10.18129/B9.bioc.markeR, R package version 1.3, https://bioconductor.org/packages/markeR. 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). diff --git a/README.md b/README.md index 521decb9..af60464f 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ across experimental and clinical phenotypes. > > Martins-Silva R, Kaizeler A, Barbosa-Morais NL (2025). *markeR: An R > Toolkit for Evaluating Gene Signatures as Phenotypic Markers*. -> , R package version 1.2, +> , R package version 1.3, > . The folder `inst/Paper/` is in the **paper** branch and contains all From fb00d3c0b2ed1a0b3643355ec0898b27c1eddae1 Mon Sep 17 00:00:00 2001 From: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com> Date: Mon, 15 Jun 2026 11:14:28 +0100 Subject: [PATCH 2/4] update citation and contact e-mail --- DESCRIPTION | 7 ++++--- NEWS.md | 10 ++++++++++ README.Rmd | 3 ++- README.md | 8 ++++---- inst/CITATION | 25 +++++++++++++++++++++++++ 5 files changed, 45 insertions(+), 8 deletions(-) create mode 100644 inst/CITATION diff --git a/DESCRIPTION b/DESCRIPTION index f9c30584..d206c5e9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,10 @@ Package: markeR Title: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers -Version: 1.3 +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 diff --git a/NEWS.md b/NEWS.md index 4d66e94e..4d4f6cbf 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,13 @@ +# markeR 1.3.1 (15 Jun 2026) + +## Minor Changes +- Updated the citation to the markeR paper published in NAR Genomics and Bioinformatics. +- Updated the contact email address. + +# markeR 1.2 (29 Apr, 2026) + +- Bioconductor Release 3.23 + # markeR 1.1.2 (12 Mar, 2026) ## Minor Changes diff --git a/README.Rmd b/README.Rmd index da4d6b38..a9cb984a 100644 --- a/README.Rmd +++ b/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 1.3, 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). diff --git a/README.md b/README.md index af60464f..3458761b 100644 --- a/README.md +++ b/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*. -> , R package version 1.3, -> . +> 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. The folder `inst/Paper/` is in the **paper** branch and contains all scripts and materials used in the original `markeR` paper to reproduce diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 00000000..21684a58 --- /dev/null +++ b/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" + ) +) \ No newline at end of file From e335dce086af1e8bf80c106b0ea08024bbe9ae0e Mon Sep 17 00:00:00 2001 From: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com> Date: Tue, 7 Jul 2026 10:12:26 +0100 Subject: [PATCH 3/4] fix runGSEA multiple contrasts --- R/runGSEA.R | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/R/runGSEA.R b/R/runGSEA.R index d80279c1..2018249a 100644 --- a/R/runGSEA.R +++ b/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 { From 60afe2786e79c490ebb50f269dc1a4e1c4fafbf8 Mon Sep 17 00:00:00 2001 From: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com> Date: Wed, 8 Jul 2026 12:23:21 +0100 Subject: [PATCH 4/4] Devel version 1.3.1; minor citation and contact changes. --- NEWS.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 4d4f6cbf..a749947a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,8 +1,9 @@ -# markeR 1.3.1 (15 Jun 2026) +# 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)