From 5b1fefdc7029bb542d06ce4b955d578f2fc7276c Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Tue, 10 Mar 2026 09:17:28 +0000
Subject: [PATCH] docs: Weekly AI README upgrade (2026-03-10)

---
 README.md | 43 +++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 41 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 430763a..ab52e09 100644
--- a/README.md
+++ b/README.md
@@ -2,8 +2,7 @@
 
 [![Codecov test coverage](https://codecov.io/github/Vitek-Lab/MSstatsBioNet/graph/badge.svg?token=SCPSPMTOEF)](https://codecov.io/github/Vitek-Lab/MSstatsBioNet)
 
-This package provides a suite of functions to query various network databases, 
-filter queries & results, and visualize networks.
+This package provides a suite of functions to query various network databases, filter queries & results, and visualize networks.
 
 ## Installation Instructions
 
@@ -88,6 +87,46 @@ print(head(subnetwork$nodes))
 print(head(subnetwork$edges))
 ```
 
+### Preview Network in Browser
+
+Quickly preview your network in a web browser using `previewNetworkInBrowser`.
+
+```r
+# Preview the network in a browser
+previewNetworkInBrowser(nodes, edges)
+```
+
+### Integrate with Shiny
+
+Use `cytoscapeNetworkOutput` and `renderCytoscapeNetwork` to integrate network visualization into a Shiny app.
+
+```r
+library(shiny)
+
+ui <- fluidPage(
+  cytoscapeNetworkOutput("cytoNetwork")
+)
+
+server <- function(input, output, session) {
+  output$cytoNetwork <- renderCytoscapeNetwork({
+    nodes <- data.frame(
+      id = c("TP53", "MDM2", "CDKN1A"),
+      logFC = c(1.5, -0.8, 2.1),
+      stringsAsFactors = FALSE
+    )
+    edges <- data.frame(
+      source = c("TP53", "MDM2"),
+      target = c("MDM2", "TP53"),
+      interaction = c("Activation", "Inhibition"),
+      stringsAsFactors = FALSE
+    )
+    cytoscapeNetwork(nodes, edges)
+  })
+}
+
+shinyApp(ui, server)
+```
+
 ## License
 This package is distributed under the [Artistic-2.0](https://opensource.org/licenses/Artistic-2.0) license. However, its dependencies may have different licenses.