From e9f67c305a6091477b18d56532a0e93172755415 Mon Sep 17 00:00:00 2001
From: leopoldguyot <leopold.guyot13@gmail.com>
Date: Tue, 23 Apr 2024 20:08:27 +0200
Subject: [PATCH] [FIX] - change vignettes to pass BiocCheck (vignettes not
 remade yet)

---
 vignettes/import_section.Rmd |  2 +-
 vignettes/scpGUI.Rmd         | 18 ++++++++++--------
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/vignettes/import_section.Rmd b/vignettes/import_section.Rmd
index daeba81..ad5d8f4 100644
--- a/vignettes/import_section.Rmd
+++ b/vignettes/import_section.Rmd
@@ -11,7 +11,7 @@ output:
         code_folding: show
 bibliography: scpGUI.bib
 date: "`r BiocStyle::doc_date()`"
-package: "`r BiocStyle::pkg_ver('scpGUI')`"
+package: "`r BiocStyle::pkg_ver('QFeaturesGUI')`"
 vignette: >
   %\VignetteIndexEntry{Import Section}
   %\VignetteEngine{knitr::rmarkdown}
diff --git a/vignettes/scpGUI.Rmd b/vignettes/scpGUI.Rmd
index 962b3c2..c5ab2a9 100644
--- a/vignettes/scpGUI.Rmd
+++ b/vignettes/scpGUI.Rmd
@@ -11,9 +11,9 @@ output:
         code_folding: show
 bibliography: scpGUI.bib
 date: "`r BiocStyle::doc_date()`"
-package: "`r BiocStyle::pkg_ver('scpGUI')`"
+package: "`r BiocStyle::pkg_ver('QFeaturesGUI')`"
 vignette: >
-  %\VignetteIndexEntry{scpGUI}
+  %\VignetteIndexEntry{QFeaturesGUI}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -26,6 +26,11 @@ knitr::opts_chunk$set(
 )
 ```
 
+
+WIP
+
+
+
 # scpGUI
 
 `scpGUI` is a shiny application that serves as a graphical interface for the [`scp` package](https://bioconductor.org/packages/release/bioc/html/scp.html) (@scpVanderaa). It leverages the power of Shiny and ShinydashboardPlus to provide a user-friendly interface for SCP data analysis. The app is organized into multiple sections, each dedicated to a specific aspect of SCP data processing. These sections are documented in separate vignettes to make it easy for users to navigate and find information relevant to their needs.
@@ -52,9 +57,9 @@ if (!require("remotes", quietly = TRUE)) {
     install.packages("remotes")
 }
 # Install the package
-remotes::install_github("UCLouvain-CBIO/scpGUI")
+#remotes::install_github("UCLouvain-CBIO/scpGUI")
 # Load the package
-library(scpGUI)
+#library(scpGUI)
 ```
 
 ## Application launch
@@ -72,12 +77,9 @@ if (interactive()) {
 When launching `scpGUI`, the user can see section of the app on the right sidebar. Each section will serve one step of the workflow.
 Each section is documented in its own vignette:
 
-- [Import Section](https://uclouvain-cbio.github.io/scpGUI/articles/import_section.html)
 
 # Citation
 
-```{r citation}
-citation("scpGUI")
-```
+
 
 # References