new version 1.1.1

Author: ritamtbsilva

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: markeR
 Title: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: 
     c(
       person("Rita", "Martins-Silva", 

NEWS.md

@@ -1,12 +1,9 @@
-# markeR 1.1.0 (11 Mar, 2026) 
-
-- Added `p.adjust.method` parameter to `runGSEA()`, `VariableAssociation()`,  `Heatmap_Cohen()`,
-
-
-enabling selection of
-  alternative multiple testing correction methods beyond the default
-  Benjamini-Hochberg FDR, including Holm-Bonferroni, Hommel, and
-  Benjamini-Yekutieli procedures.
+# markeR 1.1.1 (11 Mar, 2026) 
+ 
+  - Added `p.adjust.method` parameter across all functions performing or
+  depending on multiple testing correction, allowing users to specify
+  any correction method supported by `stats::p.adjust()`, beyond the default 
+  Benjamini-Hochberg FDR.
 - Added Python bridge scripts in `inst/python/` for users who wish to call
   markeR from a Python environment via `rpy2`. Includes a tutorial workflow
   script and a generic command-line wrapper capable of invoking any exported

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 1.1.0, 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 1.1.1, 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).