Merge pull request #58 from DiseaseTranscriptomicsLab/devel

ritamtbsilva · web-flow · commit 7cc4518993d5 · 2025-07-18T11:37:22.000+01:00
Add version 0.99.0 tag for Bioconductor submission
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: markeR
 Title: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
-Version: 0.9.5
+Version: 0.99.0
 Authors@R: 
     c(
       person("Rita", "Martins-Silva", 
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# markeR 0.99.0 (18 Jul, 2025)
+
+* First submission to Bioconductor
+
 # markeR 0.9.5 (18 Jul, 2025)
 
 * Added `VisualiseIndividualGenes()` wrapper to unify individual gene visualisation functions (`ExpressionHeatmap`, `ROCandAUCplot`, etc.) under a single, user-friendly interface.
diff --git a/README.Rmd b/README.Rmd
@@ -31,7 +31,7 @@ knitr::opts_chunk$set(
 
 > **To cite markeR please use:**
 >
->   Martins-Silva R, Kaizeler A, Barbosa-Morais N (2025). _markeR: an R Toolkit for Evaluating Gene Sets as Phenotypic Markers_. Gulbenkian Institute for Molecular Medicine, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. R package version 0.9.5, https://github.com/DiseaseTranscriptomicsLab/markeR.
+>   Martins-Silva R, Kaizeler A, Barbosa-Morais N (2025). _markeR: an R Toolkit for Evaluating Gene Sets as Phenotypic Markers_. Gulbenkian Institute for Molecular Medicine, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. R package version 0.99.0, https://github.com/DiseaseTranscriptomicsLab/markeR.
  
 `inst/Paper/` — Contains all scripts and materials used in the original markeR paper to reproduce analyses and figures.
 
diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ along with tools to compute performance metrics and visualize results.
 > Martins-Silva R, Kaizeler A, Barbosa-Morais N (2025). *markeR: an R
 > Toolkit for Evaluating Gene Sets as Phenotypic Markers*. Gulbenkian
 > Institute for Molecular Medicine, Faculdade de Medicina, Universidade
-> de Lisboa, Lisbon, Portugal. R package version 0.9.5,
+> de Lisboa, Lisbon, Portugal. R package version 0.99.0,
 > <https://github.com/DiseaseTranscriptomicsLab/markeR>.
 
 `inst/Paper/` — Contains all scripts and materials used in the original
diff --git a/inst/CITATION b/inst/CITATION
@@ -11,6 +11,6 @@ bibentry(
   organization = "Gulbenkian Institute for Molecular Medicine, Faculdade de Medicina, Universidade de Lisboa",
   address = "Lisbon, Portugal",
   year = format(Sys.Date(), "%Y"),
-  note = "R package version 0.9.5",
+  note = "R package version 0.99.0",
   url = "https://github.com/DiseaseTranscriptomicsLab/markeR"
 )

Original file line number	Diff line number	Diff line change
`@@ -31,7 +31,7 @@ knitr::opts_chunk$set(`
`31`	`31`
`32`	`32`	`> To cite markeR please use:`
`33`	`33`	`>`
`34`		`-> Martins-Silva R, Kaizeler A, Barbosa-Morais N (2025). _markeR: an R Toolkit for Evaluating Gene Sets as Phenotypic Markers_. Gulbenkian Institute for Molecular Medicine, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. R package version 0.9.5, https://github.com/DiseaseTranscriptomicsLab/markeR.`
	`34`	`+> Martins-Silva R, Kaizeler A, Barbosa-Morais N (2025). _markeR: an R Toolkit for Evaluating Gene Sets as Phenotypic Markers_. Gulbenkian Institute for Molecular Medicine, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. R package version 0.99.0, https://github.com/DiseaseTranscriptomicsLab/markeR.`
`35`	`35`
`36`	`36`	`inst/Paper/` — Contains all scripts and materials used in the original markeR paper to reproduce analyses and figures.
`37`	`37`
Original file line number	Diff line number	Diff line change
`@@ -11,6 +11,6 @@ bibentry(`
`11`	`11`	`organization = "Gulbenkian Institute for Molecular Medicine, Faculdade de Medicina, Universidade de Lisboa",`
`12`	`12`	`address = "Lisbon, Portugal",`
`13`	`13`	`year = format(Sys.Date(), "%Y"),`
`14`		`- note = "R package version 0.9.5",`
	`14`	`+ note = "R package version 0.99.0",`
`15`	`15`	`url = "https://github.com/DiseaseTranscriptomicsLab/markeR"`
`16`	`16`	`)`