Merge pull request #77 from DiseaseTranscriptomicsLab/main

Bioconductor release

Author: ritamtbsilva

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: markeR
 Title: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
-Version: 0.99.5
+Version: 1.1.0
 Authors@R: 
     c(
       person("Rita", "Martins-Silva", 
@@ -14,10 +14,11 @@ Authors@R:
                comment=c(ORCID="0000-0002-1215-0538"))
     )
 Description: 
-    A suite of methods for using gene sets 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

README.Rmd

@@ -17,20 +17,20 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 
-![](https://img.shields.io/badge/status-development-yellowgreen)
+<!--![](https://img.shields.io/badge/status-development-yellowgreen)-->
 [![Pkgdown](https://img.shields.io/badge/docs-pkgdown-blue.svg)](https://diseasetranscriptomicslab.github.io/markeR/)
 ![Minimal R Version](https://img.shields.io/badge/min%20R-4.5.0-blue.svg)
 [![codecov](https://codecov.io/gh/DiseaseTranscriptomicsLab/markeR/graph/badge.svg?token=7T1I4JCJG6)](https://codecov.io/gh/DiseaseTranscriptomicsLab/markeR)
-[![R-CMD-check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml)
-[![Bioconductor Check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml)
+<!-- [![R-CMD-check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml)-->
+<!-- [![Bioconductor Check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml) -->
 
 <!-- badges: end -->
 
 **`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.
 
 > **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 0.99.5, 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 1.0.0, https://github.com/DiseaseTranscriptomicsLab/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).
 
@@ -57,8 +57,20 @@ The folder `inst/Paper/` is in the **paper** branch and contains all scripts and
 
 ## Installation 
 
-Install the latest development release of markeR from [GitHub](https://github.com/) with:
 
+Install the latest release from Bioconductor:
+
+```{r, eval=FALSE}
+# Install from Bioconductor
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install("markeR")
+library(markeR)
+```
+ 
+
+Or install the latest development release of `markeR` from [GitHub](https://github.com/) with:
+   
 ``` r
 # install.packages("devtools")
 devtools::install_github("DiseaseTranscriptomicsLab/markeR@*release")

README.md

@@ -5,14 +5,14 @@
 
 <!-- badges: start -->
 
-![](https://img.shields.io/badge/status-development-yellowgreen)
+<!--![](https://img.shields.io/badge/status-development-yellowgreen)-->
+
 [![Pkgdown](https://img.shields.io/badge/docs-pkgdown-blue.svg)](https://diseasetranscriptomicslab.github.io/markeR/)
 ![Minimal R
 Version](https://img.shields.io/badge/min%20R-4.5.0-blue.svg)
 [![codecov](https://codecov.io/gh/DiseaseTranscriptomicsLab/markeR/graph/badge.svg?token=7T1I4JCJG6)](https://codecov.io/gh/DiseaseTranscriptomicsLab/markeR)
-[![R-CMD-check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml)
-[![Bioconductor
-Check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml)
+<!-- [![R-CMD-check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml)-->
+<!-- [![Bioconductor Check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml) -->
 
 <!-- badges: end -->
 
@@ -27,7 +27,7 @@ across experimental and clinical phenotypes.
 > 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 0.99.5,
+> de Lisboa, Lisbon, Portugal. R package version 1.0.0,
 > <https://github.com/DiseaseTranscriptomicsLab/markeR>.
 
 The folder `inst/Paper/` is in the **paper** branch and contains all
@@ -58,7 +58,18 @@ analyses and figures. You can browse it
 
 ## Installation
 
-Install the latest development release of markeR from [GitHub](https://github.com/) with:
+Install the latest release from Bioconductor:
+
+``` r
+# Install from Bioconductor
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install("markeR")
+library(markeR)
+```
+
+Or install the latest development release of `markeR` from
+[GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")

vignettes/markeR.Rmd

@@ -53,7 +53,16 @@ The package is implemented with flexibility and extensibility as core design pri
 
 # Installation
 
-Install the latest development release of `markeR` from [GitHub](https://github.com/) with:
+Install the latest release from Bioconductor:
+
+```{r, eval=FALSE}
+# Install from Bioconductor
+if (!requireNamespace("BiocManager", quietly = TRUE))
+  install.packages("BiocManager")
+BiocManager::install("markeR")
+```
+
+Or install the latest development release of `markeR` from [GitHub](https://github.com/) with:
 
 ```r
 devtools::install_github("DiseaseTranscriptomicsLab/markeR@*release")