Breeding-Insight · Cristianetaniguti · Apr 22, 2026 · Apr 22, 2026 · Apr 22, 2026 · Apr 22, 2026
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Breedverse
 Title: Collection of R Shiny Packages From Breeding Insight
-Version: 0.2.0
+Version: 0.3.0
 Authors@R: c(person(given='Cristiane', 
                     family='Taniguti', 
                     email = 'ctaniguti@ufl.edu', 
@@ -18,7 +18,7 @@ Authors@R: c(person(given='Cristiane',
                     family='Insight', 
                     role = 'aut')
              )
-Description: Provides an interface for users to add modules from BIGapp, Qploidy, familia and AlloMate packages.
+Description: Provides an interface for users to add modules from BIGapp, Qploidy, familia, GenoBrew and AlloMate packages.
 License: Apache License 2.0
 Depends: R (>= 3.6.0)
 biocViews:
@@ -43,12 +43,13 @@ Suggests:
     Qploidy,
     BIGapp,
     familia,
-    AlloMate
+    GenoBrew
 Remotes:
     Cristianetaniguti/Qploidy,
     Breeding-Insight/BIGapp,
     Breeding-Insight/familia,
-    Breeding-Insight/AlloMate@development
+    Breeding-Insight/AlloMate@development,
+    Breeding-Insight/GenoBrew@development
 URL: https://github.com/Breeding-Insight/Breedverse
 BugReports: https://github.com/Breeding-Insight/Breedverse/issues
 LazyData: true

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,9 @@
 # breedverse NEWS
 
+## breedverse 0.3.0
+
+* Add GenoBrew
+
 ## breedverse 0.2.0
 
 * Collapse packages modules into a single collapsible menuItem in the left side menu

diff --git a/R/app_server.R b/R/app_server.R
@@ -17,24 +17,30 @@ app_server <- function(input, output, session) {
   output$qploidyInstalled <- reactive({
     "Qploidy" %in% rownames(installed.packages())
   })
-  
+
   output$BIGappInstalled <- reactive({
     "BIGapp" %in% rownames(installed.packages())
   })
-  
+
   output$familiaInstalled <- reactive({
     "familia" %in% rownames(installed.packages())
   })
-  
+
   output$allomateInstalled <- reactive({
     "AlloMate" %in% rownames(installed.packages())
   })
-
+
+  output$genobrewInstalled <- reactive({
+    "GenoBrew" %in% rownames(installed.packages())
+  })
+
   # Expose the value to JS even when panel is hidden
   outputOptions(output, "qploidyInstalled", suspendWhenHidden = FALSE)
   outputOptions(output, "BIGappInstalled", suspendWhenHidden = FALSE)
   outputOptions(output, "familiaInstalled", suspendWhenHidden = FALSE)
   outputOptions(output, "allomateInstalled", suspendWhenHidden = FALSE)
+  outputOptions(output, "genobrewInstalled", suspendWhenHidden = FALSE)
+
 
   ## Modules
 
@@ -47,17 +53,17 @@ app_server <- function(input, output, session) {
   callModule(mod_install_server,
              "install_1",
              parent_session = session)
-  
+
   ## Qploidy
   if(isTRUE(requireNamespace("Qploidy", quietly = TRUE))) {
     do.call("library", list("Qploidy"))
     callModule(getFromNamespace("mod_qploidy_server", "Qploidy"),
                "qploidy_1",
                parent_session = session)
-  } 
-  
+  }
+
   ## BIGapp
-  
+
   if(isTRUE(requireNamespace("BIGapp", quietly = TRUE))) {
     do.call("library", list("BIGapp"))
     callModule(getFromNamespace("mod_DosageCall_server", "BIGapp"),
@@ -85,9 +91,9 @@ app_server <- function(input, output, session) {
                "GS_1",
                parent_session = session)
   }
-  
+
   ##familia
-  
+
   if(isTRUE(requireNamespace("familia", quietly = TRUE))) {
     do.call("library", list("familia"))
     callModule(getFromNamespace("mod_SNMF_server", "familia"),
@@ -97,16 +103,27 @@ app_server <- function(input, output, session) {
                "PolyBreedTools_1",
                parent_session = session)
   }
-  
+
   ## AlloMate
   if(isTRUE(requireNamespace("AlloMate", quietly = TRUE))) {
     do.call("library", list("AlloMate"))
     getFromNamespace("mod_allomate_server", "AlloMate")(
       "allomate_1",
       parent_session = session
     )
-  } 
-
+  }
+
+  ## GenoBrew
+  if(isTRUE(requireNamespace("GenoBrew", quietly = TRUE))) {
+    do.call("library", list("GenoBrew"))
+    callModule(getFromNamespace("mod_mk_select_server", "GenoBrew"),
+               "mk_select_1",
+               parent_session = session)
+    callModule(getFromNamespace("mod_cnv_server", "GenoBrew"),
+               "cnv_1",
+               parent_session = session)
+  }
+
   #Session info popup
   observeEvent(input$session_info_button, {
     showModal(modalDialog(
@@ -122,13 +139,13 @@ app_server <- function(input, output, session) {
       )
     ))
   })
-  
+
   #Check for updates from GitHub for Breedverse
   get_latest_github_commit <- function(repo, owner) {
     url <- paste0("https://api.github.com/repos/", owner, "/", repo, "/releases/latest")
     response <- GET(url)
     content <- content(response, "parsed")
-    
+
     if (status_code(response) == 200) {
       tag_name <- content$tag_name
       clean_tag_name <- sub("-.*", "", tag_name)
@@ -138,7 +155,7 @@ app_server <- function(input, output, session) {
       return(NULL)
     }
   }
-  
+
   is_internet_connected <- function() {
     handle <- new_handle()
     success <- tryCatch({
@@ -149,7 +166,7 @@ app_server <- function(input, output, session) {
     })
     return(success)
   }
-  
+
   observeEvent(input$updates_info_button, {
     # Check internet connectivity
     if (!is_internet_connected()) {
@@ -164,17 +181,17 @@ app_server <- function(input, output, session) {
       ))
       return()
     }
-    
+
     package_name <- "Breedverse"
     repo_name <- "Breedverse" # GitHub repo name
     repo_owner <- "Breeding-Insight" # User or organization name
-    
+
     # Get the installed version
     installed_version <- as.character(packageVersion(package_name))
-    
+
     # Get the latest version from GitHub (can be tag version or latest commit)
     latest_commit <- get_latest_github_commit(repo_name, repo_owner)
-    
+
     # Compare versions and prepare message
     if (latest_commit > installed_version) {
       update_status <- "A new version is available. Please update your package."
@@ -194,7 +211,7 @@ app_server <- function(input, output, session) {
         update_status
       )
     }
-    
+
     # Display message in a Shiny modal
     showModal(modalDialog(
       title = "Breedverse Updates",

diff --git a/R/app_ui.R b/R/app_ui.R
@@ -57,13 +57,13 @@ app_ui <- function(request) {
                     tags$li(class = "header", style = "color: grey; margin-top: 10px; margin-bottom: 10px; padding-left: 15px;", "Menu"),
                     menuItem("Home", tabName = "welcome", icon = icon("house"),startExpanded = FALSE),
                     menuItem("Install modules", tabName = "install", icon = icon("share-from-square")),
-                    
+
                     conditionalPanel(
                       condition = "output.qploidyInstalled == true",
                       tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Ploidy Estimation"),
                       menuItem("Qploidy", tabName = "qploidy", icon = icon("dna")),
                     ),
-                    
+
                     conditionalPanel(
                       condition = "output.familiaInstalled == true",
                       tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Ancestry (R/familia)"),
@@ -75,13 +75,13 @@ app_ui <- function(request) {
                         menuSubItem("Unsupervised", tabName = "polybreedtools", icon = icon("share-from-square"))
                       )
                     ),
-                    
+
                     conditionalPanel(
                       condition = "output.allomateInstalled == true",
                       tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Mating Estimation (R/AlloMate)"),
                       menuItem("AlloMate", tabName = "allomate", icon = icon("diagram-project"))
                     ),
-                    
+
                     conditionalPanel(
                       condition = "output.BIGappInstalled == true",
                       tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Genotype Processing"),
@@ -100,7 +100,18 @@ app_ui <- function(request) {
                         menuSubItem("Genomic Prediction", tabName = "prediction", icon = icon("angles-right"))
                       )
                     ),
-
+                    conditionalPanel(
+                      condition = "output.genobrewInstalled == true",
+                      tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Marker Panel Test &\n CNV Profiles"),
+                      menuItem(
+                        "GenoBrew",
+                        icon = icon("dna"),
+                        startExpanded = FALSE,
+                        menuSubItem("Select Markers", tabName = "mk_select", icon = icon("magnifying-glass")),
+                        menuSubItem("CNV profiles", tabName = "cnv", icon = icon("dna"))
+                      )
+                    ),
+
                     tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Information"),
                     menuItem("Source Code", icon = icon("circle-info"), href = "https://www.github.com/Breeding-Insight/Genomics_Shiny_App"),
                     menuItem("Help", tabName = "help", icon = icon("circle-question"))
@@ -128,7 +139,7 @@ app_ui <- function(request) {
           )
         ),
         left = div(
-          style = "display: flex; align-items: center; height: 100%;",  
+          style = "display: flex; align-items: center; height: 100%;",
           sprintf("v%s", as.character(utils::packageVersion("Breedverse"))))
       ),
       dashboardBody(
@@ -155,70 +166,80 @@ app_ui <- function(request) {
             tabName = "install", mod_install_ui("install_1")
           ),
           tabItem(
-            tabName = "qploidy", 
-            if(isTRUE(requireNamespace("Qploidy", quietly = TRUE))) 
+            tabName = "qploidy",
+            if(isTRUE(requireNamespace("Qploidy", quietly = TRUE)))
               getFromNamespace("mod_qploidy_ui", "Qploidy")("qploidy_1")
           ),
           tabItem(
-            tabName = "snmf", 
-            if(isTRUE(requireNamespace("familia", quietly = TRUE))) 
+            tabName = "snmf",
+            if(isTRUE(requireNamespace("familia", quietly = TRUE)))
               getFromNamespace("mod_SNMF_ui", "familia")("SNMF_1")
           ),
           tabItem(
-            tabName = "polybreedtools", 
-            if(isTRUE(requireNamespace("familia", quietly = TRUE))) 
+            tabName = "polybreedtools",
+            if(isTRUE(requireNamespace("familia", quietly = TRUE)))
               getFromNamespace("mod_polybreedtools_ui", "familia")("PolyBreedTools_1")
           ),
           tabItem(
-            tabName = "allomate", 
-            if(isTRUE(requireNamespace("AlloMate", quietly = TRUE))) 
+            tabName = "allomate",
+            if(isTRUE(requireNamespace("AlloMate", quietly = TRUE)))
               getFromNamespace("mod_allomate_ui", "AlloMate")("allomate_1")
           ),
           tabItem(
-            tabName = "filtering", 
-            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE))) 
+            tabName = "filtering",
+            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE)))
               getFromNamespace("mod_Filtering_ui", "BIGapp")("Filtering_1")
           ),
           tabItem(
-            tabName = "updog", 
-            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE))) 
+            tabName = "updog",
+            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE)))
               getFromNamespace("mod_DosageCall_ui", "BIGapp")("DosageCall_1")
           ),
           tabItem(
-            tabName = "dosage2vcf", 
-            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE))) 
+            tabName = "dosage2vcf",
+            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE)))
               getFromNamespace("mod_dosage2vcf_ui", "BIGapp")("dosage2vcf_1")
           ),
           tabItem(
-            tabName = "pca", 
-            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE))) 
+            tabName = "pca",
+            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE)))
               getFromNamespace("mod_PCA_ui", "BIGapp")("PCA_1")
           ),
           tabItem(
-            tabName = "dapc", 
-            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE))) 
+            tabName = "dapc",
+            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE)))
               getFromNamespace("mod_dapc_ui", "BIGapp")("dapc_1")
           ),
           tabItem(
-            tabName = "gwas", 
-            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE))) 
+            tabName = "gwas",
+            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE)))
               getFromNamespace("mod_gwas_ui", "BIGapp")("gwas_1")
           ),
           tabItem(
-            tabName = "diversity", 
-            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE))) 
+            tabName = "diversity",
+            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE)))
               getFromNamespace("mod_diversity_ui", "BIGapp")("diversity_1")
           ),
           tabItem(
             tabName = "prediction_accuracy",
-            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE))) 
+            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE)))
               getFromNamespace("mod_GSAcc_ui", "BIGapp")("GSAcc_1")
           ),
           tabItem(
-            tabName = "prediction", 
-            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE))) 
+            tabName = "prediction",
+            if(isTRUE(requireNamespace("BIGapp", quietly = TRUE)))
               getFromNamespace("mod_GS_ui", "BIGapp")("GS_1")
           ),
+          tabItem(
+            tabName = "mk_select",
+            if(isTRUE(requireNamespace("GenoBrew", quietly = TRUE)))
+              getFromNamespace("mod_mk_select_ui", "GenoBrew")("mk_select_1")
+          ),
+          tabItem(
+            tabName = "cnv",
+            if(isTRUE(requireNamespace("GenoBrew", quietly = TRUE)))
+              getFromNamespace("mod_cnv_ui", "GenoBrew")("cnv_1")
+          ),
           tabItem(
             tabName = "help", mod_help_ui("help_1")
           )
@@ -241,7 +262,7 @@ golem_add_external_resources <- function() {
     "www",
     app_sys("app/www")
   )
-  
+
   tags$head(
     favicon(),
     bundle_resources(