diff --git a/doc/pagoda2.walkthrough.Rmd b/doc/pagoda2.walkthrough.Rmd
index 5e13421..db4626d 100644
--- a/doc/pagoda2.walkthrough.Rmd
+++ b/doc/pagoda2.walkthrough.Rmd
@@ -389,7 +389,7 @@ This app will now be viewable as long as our R session is running. However we al
 
 Users may also interactively explore [Conos](https://github.com/kharchenkolab/conos) objects with the Pagoda2 application.
 
-After constructing the Conos object `con` as shown in the Conos [walkthrough](https://github.com/kharchenkolab/conos/blob/master/doc/walkthrough.md), users can save to a serialized `*.bin` file and upload into the pagoda application with the `p2app4conos()` function, using `p2app4conos(conos=con)`. Please see Conos for more details.
+After constructing the Conos object `con` as shown in the Conos [walkthrough](https://github.com/kharchenkolab/conos/blob/main/doc/walkthrough.md), users can save to a serialized `*.bin` file and upload into the pagoda application with the `p2app4conos()` function, using `p2app4conos(conos=con)`. Please see Conos for more details.
 
 ### More Details
 
diff --git a/doc/pagoda2.walkthrough.html b/doc/pagoda2.walkthrough.html
index 4eab094..c1332fd 100644
--- a/doc/pagoda2.walkthrough.html
+++ b/doc/pagoda2.walkthrough.html
@@ -724,7 +724,7 @@ <h3>View Conos Object in Pagoda2 Frontend Application</h3>
 
 <p>Users may also interactively explore <a href="https://github.com/kharchenkolab/conos">Conos</a> objects with the Pagoda2 application.</p>
 
-<p>After constructing the Conos object <code>con</code> as shown in the Conos <a href="https://github.com/kharchenkolab/conos/blob/master/doc/walkthrough.md">walkthrough</a>, users can save to a serialized <code>*.bin</code> file and upload into the pagoda application with the <code>p2app4conos()</code> function, using <code>p2app4conos(conos=con)</code>. Please see Conos for more details.</p>
+<p>After constructing the Conos object <code>con</code> as shown in the Conos <a href="https://github.com/kharchenkolab/conos/blob/main/doc/walkthrough.md">walkthrough</a>, users can save to a serialized <code>*.bin</code> file and upload into the pagoda application with the <code>p2app4conos()</code> function, using <code>p2app4conos(conos=con)</code>. Please see Conos for more details.</p>
 
 <h3>More Details</h3>
 
diff --git a/doc/pagoda2.walkthrough.md b/doc/pagoda2.walkthrough.md
index a00f5e5..1b588cc 100644
--- a/doc/pagoda2.walkthrough.md
+++ b/doc/pagoda2.walkthrough.md
@@ -623,7 +623,7 @@ This app will now be viewable as long as our R session is running. However we al
 
 Users may also interactively explore [Conos](https://github.com/kharchenkolab/conos) objects with the Pagoda2 application.
 
-After constructing the Conos object `con` as shown in the Conos [walkthrough](https://github.com/kharchenkolab/conos/blob/master/doc/walkthrough.md), users can save to a serialized `*.bin` file and upload into the pagoda application with the `p2app4conos()` function, using `p2app4conos(conos=con)`. Please see Conos for more details.
+After constructing the Conos object `con` as shown in the Conos [walkthrough](https://github.com/kharchenkolab/conos/blob/main/doc/walkthrough.md), users can save to a serialized `*.bin` file and upload into the pagoda application with the `p2app4conos()` function, using `p2app4conos(conos=con)`. Please see Conos for more details.
 
 ### More Details