Main

.Rbuildignore

@@ -19,3 +19,6 @@
 ^\\.github$
 ^\\.git$
 ^codecov\.yml$
+^vignettes/articles$
+^data_aux$ 
+^python(/.*)?$

.github/workflows/R-CMD-check.yaml

@@ -2,8 +2,14 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, default]
   pull_request:
+    branches: [main, default]
+  release:
+    types: [published]
+    branches: [main, default]
+  workflow_dispatch:
+    branches: [main, default]
 
 name: R-CMD-check.yaml
 
@@ -48,6 +54,7 @@ jobs:
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: '"error"'
 
       - name: Test coverage
         if: runner.os == 'Linux' && matrix.config.r == 'release'

.github/workflows/bioc-check.yml

@@ -2,9 +2,14 @@ name: Bioconductor Check
 
 on:
   push:
-    branches: [main, master]
+    branches: [main, default]
   pull_request:
-    branches: [main, master]
+    branches: [main, default]
+  release:
+    types: [published]
+    branches: [main, default]
+  workflow_dispatch:
+    branches: [main, default]
 
 jobs:
   bioccheck:
@@ -13,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        r-version: ['4.4.0','4.5.0']
+        r-version: ['4.5.0']
 
     steps:
       - uses: actions/checkout@v4
@@ -37,4 +42,4 @@ jobs:
 
       - name: Run BiocCheck
         run: BiocCheck::BiocCheck(".", quit_with_status=TRUE)
-        shell: Rscript {0}
+        shell: Rscript {0}

.github/workflows/pkgdown.yaml

@@ -2,11 +2,14 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [default]
   pull_request:
+    branches: [default]
   release:
     types: [published]
+    branches: [default]
   workflow_dispatch:
+    branches: [default]
 
 name: pkgdown.yaml
 

.gitignore

@@ -9,11 +9,13 @@
 docs
 renv.lock
 .obsidian/
-/inst/Paper/data/ 
-/inst/Paper/localjobs/ 
 markeR.BiocCheck/ 
 /doc/
 /Meta/
 markeR.Rproj
 .DS_Store
-**/.DS_Store
+**/.DS_Store 
+inst/doc
+data_aux
+markeR.Rcheck 
+/python/.venv

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: markeR
 Title: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
-Version: 0.99.2 
+Version: 1.3
 Authors@R: 
     c(
       person("Rita", "Martins-Silva", 
@@ -14,17 +14,18 @@ Authors@R:
                comment=c(ORCID="0000-0002-1215-0538"))
     )
 Description: 
-    markeR provides a suite of methods for using gene sets (signatures) to quantify and evaluate the 
-    extent to which a given gene signature marks a specific phenotype. The package implements various 
-    scoring, enrichment and classification approaches, along with tools to compute 
-    performance metrics and visualize results, making it a valuable resource for transcriptomics research (bulk RNA-seq).
+    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.
 License: Artistic-2.0
 biocViews: GeneExpression, Transcriptomics, Visualization, Software, GeneSetEnrichment, Classification
 Encoding: UTF-8
 Language: en-GB
 LazyData: false
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Additional_repositories: https://bioconductor.org/packages/release/bioc
 Imports:
     circlize,
@@ -46,7 +47,6 @@ Imports:
     limma,
     ggrepel,
     effectsize,
-    patchwork,
     msigdbr,
     tibble
 Suggests: 
@@ -59,11 +59,14 @@ Suggests:
     rmarkdown, 
     roxygen2,
     mockery,
-    covr
+    covr,
+    magick,
+    BiocStyle
 Config/testthat/edition: 3
 Depends: 
-    R (>= 3.5.0)
+    R (>= 4.5.0)
 URL: https://diseasetranscriptomicslab.github.io/markeR/,
      https://github.com/DiseaseTranscriptomicsLab/markeR
 BugReports: https://github.com/DiseaseTranscriptomicsLab/markeR/issues
 VignetteBuilder: knitr
+Config/Needs/website: rmarkdown