docs: Weekly AI README upgrade — FAQ / Common Pitfalls (#79)

Author: github-actions[bot]

README.md

@@ -21,10 +21,77 @@ You can install the development version of this package through Github:
 devtools::install_github("Vitek-Lab/MSstatsBioNet", build_vignettes = TRUE)
 ```
 
+## Usage Examples
+
+Here are some examples to help you get started with MSstatsBioNet:
+
+### Annotate Protein Information
+
+Use the `annotateProteinInfoFromIndra` function to annotate a data frame with protein information from Indra.
+
+```r
+library(MSstatsBioNet)
+
+# Example data frame
+df <- data.frame(Protein = c("CLH1_HUMAN"))
+
+# Annotate protein information
+annotated_df <- annotateProteinInfoFromIndra(df, "Uniprot_Mnemonic")
+print(head(annotated_df))
+```
+
+### Visualize Networks with Cytoscape
+
+Create an interactive network diagram using `cytoscapeNetwork`.
+
+```r
+# Define nodes and edges
+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
+)
+
+# Render the network
+cytoscapeNetwork(nodes, edges)
+```
+
+### Export Network to HTML
+
+Export your network visualization to an HTML file using `exportNetworkToHTML`.
+
+```r
+# Export the network to an HTML file
+exportNetworkToHTML(nodes, edges, filename = "network.html")
+```
+
+### Retrieve Subnetwork from INDRA
+
+Use `getSubnetworkFromIndra` to retrieve a subnetwork of protein interactions from the INDRA database.
+
+```r
+# Load example input data
+input <- data.table::fread(system.file(
+    "extdata/groupComparisonModel.csv",
+    package = "MSstatsBioNet"
+))
+
+# Get subnetwork
+subnetwork <- getSubnetworkFromIndra(input)
+print(head(subnetwork$nodes))
+print(head(subnetwork$edges))
+```
+
 ## 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.  
+This package is distributed under the [Artistic-2.0](https://opensource.org/licenses/Artistic-2.0) license. However, its dependencies may have different licenses.  
 
-Notably, INDRA is distributed under the [BSD 2-Clause](https://opensource.org/license/bsd-2-clause) license.  Furthermore, INDRA's knowledge sources may have different licenses for commercial applications.  Please refer to the [INDRA README](https://github.com/sorgerlab/indra?tab=readme-ov-file#indra-modules) for more information on its knowledge sources and their associated licenses.
+Notably, INDRA is distributed under the [BSD 2-Clause](https://opensource.org/license/bsd-2-clause) license. Furthermore, INDRA's knowledge sources may have different licenses for commercial applications. Please refer to the [INDRA README](https://github.com/sorgerlab/indra?tab=readme-ov-file#indra-modules) for more information on its knowledge sources and their associated licenses.
 
 ## Databases Supported
 
@@ -36,4 +103,4 @@ Notably, INDRA is distributed under the [BSD 2-Clause](https://opensource.org/li
 
 ## Visualization Options Supported
 
-- Cytoscape Desktop 
+- Cytoscape Desktop