--- a/COBRAxy/docs/getting-started.md	Mon Oct 27 12:33:08 2025 +0000
+++ b/COBRAxy/docs/getting-started.md	Tue Oct 28 10:44:07 2025 +0000
@@ -74,7 +74,6 @@
 
 ```bash
 # Generate RAS from expression data
-# Note: -td is optional and auto-detected after pip install
 ras_generator \
   -in expression_data.tsv \
   -ra ras_output.tsv \
@@ -85,7 +84,6 @@
 
 ```bash
 # Generate enriched pathway maps
-# Note: -td is optional and auto-detected after pip install
 marea \
   -using_RAS true \
   -input_data ras_output.tsv \
@@ -138,13 +136,12 @@
 
 Now that you understand the basics:
 
-1. **[Quick Start Guide](/quickstart.md)** - Complete walkthrough with example data
-2. **[Galaxy Tutorial](/tutorials/galaxy-setup.md)** - Web-based analysis setup
+1. **[Quick Start Guide](quickstart)** - Complete walkthrough with example data
+2. **[Galaxy Tutorial](tutorials/galaxy-setup)** - Web-based analysis setup
 3. **[Tools Reference](/tools/)** - Detailed documentation for each tool
-4. **[Examples](/examples/)** - Real-world analysis examples
 
 ## Need Help?
 
-- **[Troubleshooting](/troubleshooting.md)** - Common issues and solutions
+- **[Troubleshooting](troubleshooting)** - Common issues and solutions
 - **[GitHub Issues](https://github.com/CompBtBs/COBRAxy/issues)** - Report bugs or ask questions
-- **[Contributing](/contributing.md)** - Help improve COBRAxy
\ No newline at end of file
+- **[Contributing](contributing)** - Help improve COBRAxy
\ No newline at end of file