diff --git a/articles/iSEEbug.html b/articles/iSEEbug.html
index 81321ee..45d9498 100644
--- a/articles/iSEEbug.html
+++ b/articles/iSEEbug.html
@@ -69,7 +69,7 @@
       <h1 data-toc-skip>iSEEbug</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/devel/vignettes/iSEEbug.Rmd" class="external-link"><code>vignettes/iSEEbug.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/transform/vignettes/iSEEbug.Rmd" class="external-link"><code>vignettes/iSEEbug.Rmd</code></a></small>
       <div class="hidden name"><code>iSEEbug.Rmd</code></div>
 
     </div>
diff --git a/authors.html b/authors.html
index a75e5bb..dc9bc91 100644
--- a/authors.html
+++ b/authors.html
@@ -56,7 +56,7 @@ <h1>Authors and Citation</h1>
     <div class="section level2 citation-section">
     <div>
       <h1 id="citation">Citation</h1>
-      <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/devel/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/transform/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small>
     </div>
     </div>
 
diff --git a/pkgdown.yml b/pkgdown.yml
index f83902e..581b22a 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,4 +3,4 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   iSEEbug: iSEEbug.html
-last_built: 2024-10-02T08:10Z
+last_built: 2024-10-23T12:54Z
diff --git a/reference/create_observers.html b/reference/create_observers.html
index 8eb373a..9ee0a17 100644
--- a/reference/create_observers.html
+++ b/reference/create_observers.html
@@ -46,7 +46,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Observers</h1>
-    <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/devel/R/observers.R" class="external-link"><code>R/observers.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/transform/R/observers.R" class="external-link"><code>R/observers.R</code></a></small>
     <div class="hidden name"><code>create_observers.Rd</code></div>
     </div>
 
@@ -57,7 +57,13 @@ <h1>Observers</h1>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">.create_observers</span><span class="op">(</span><span class="va">input</span>, <span class="va">session</span>, <span class="va">rObjects</span><span class="op">)</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">.create_import_observers</span><span class="op">(</span><span class="va">input</span>, <span class="va">rObjects</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">.create_manipulate_observers</span><span class="op">(</span><span class="va">input</span>, <span class="va">rObjects</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">.create_estimate_observers</span><span class="op">(</span><span class="va">input</span>, <span class="va">rObjects</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">.update_observers</span><span class="op">(</span><span class="va">input</span>, <span class="va">session</span>, <span class="va">rObjects</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">.create_launch_observers</span><span class="op">(</span><span class="va">FUN</span>, <span class="va">input</span>, <span class="va">session</span>, <span class="va">rObjects</span><span class="op">)</span></span></code></pre></div>
     </div>
diff --git a/reference/iSEEbug.html b/reference/iSEEbug.html
index 00f3eac..8edefe3 100644
--- a/reference/iSEEbug.html
+++ b/reference/iSEEbug.html
@@ -46,14 +46,14 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>iSEEbug</h1>
-    <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/devel/R/iSEEbug.R" class="external-link"><code>R/iSEEbug.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/transform/R/iSEEbug.R" class="external-link"><code>R/iSEEbug.R</code></a></small>
     <div class="hidden name"><code>iSEEbug.Rd</code></div>
     </div>
 
     <div class="ref-description">
     <p>iSEEbug is a web app that provides an interface to build and explore
 <code><a href="https://rdrr.io/pkg/TreeSummarizedExperiment/man/TreeSummarizedExperiment-constructor.html" class="external-link">TreeSummarizedExperiment</a></code>
-(TreeSE) objects by means of <a href="https://rdrr.io/pkg/iSEE/man/iSEE.html" class="external-link">iSEE</a>.</p>
+(TreeSE) objects by means of <a href="https://isee.github.io/iSEE/reference/iSEE.html" class="external-link">iSEE</a>.</p>
     </div>
 
     <div id="ref-usage">
@@ -62,12 +62,12 @@ <h1>iSEEbug</h1>
 
     <div id="value">
     <h2>Value</h2>
-    <p>An <code><a href="https://rdrr.io/pkg/iSEE/man/iSEE.html" class="external-link">iSEE</a></code> app with a custom landing page to
+    <p>An <code><a href="https://isee.github.io/iSEE/reference/iSEE.html" class="external-link">iSEE</a></code> app with a custom landing page to
 build TreeSE objects and explore <a href="https://rdrr.io/pkg/mia/man/mia-datasets.html" class="external-link">mia datasets</a>.</p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
-    <div class="dont-index"><p><a href="https://rdrr.io/pkg/iSEE/man/iSEE.html" class="external-link">iSEE</a> <a href="https://rdrr.io/pkg/mia/man/mia-package.html" class="external-link">mia</a>
+    <div class="dont-index"><p><a href="https://isee.github.io/iSEE/reference/iSEE.html" class="external-link">iSEE</a> <a href="https://rdrr.io/pkg/mia/man/mia-package.html" class="external-link">mia</a>
 <a href="https://rdrr.io/pkg/miaViz/man/miaViz-package.html" class="external-link">miaViz</a></p></div>
     </div>
 
diff --git a/reference/landing_page.html b/reference/landing_page.html
index ce13e5f..cb8f683 100644
--- a/reference/landing_page.html
+++ b/reference/landing_page.html
@@ -45,7 +45,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Landing page</h1>
-    <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/devel/R/landing_page.R" class="external-link"><code>R/landing_page.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/transform/R/landing_page.R" class="external-link"><code>R/landing_page.R</code></a></small>
     <div class="hidden name"><code>landing_page.Rd</code></div>
     </div>
 
diff --git a/reference/render_output.html b/reference/render_output.html
index 9d1edf5..293e767 100644
--- a/reference/render_output.html
+++ b/reference/render_output.html
@@ -46,7 +46,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Outputs</h1>
-    <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/devel/R/outputs.R" class="external-link"><code>R/outputs.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/RiboRings/iSEEbug/blob/transform/R/outputs.R" class="external-link"><code>R/outputs.R</code></a></small>
     <div class="hidden name"><code>render_output.Rd</code></div>
     </div>