diff --git a/404.html b/404.html
index 01727e6..5f6c7eb 100644
--- a/404.html
+++ b/404.html
@@ -21,7 +21,13 @@
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script src="https://sigven.github.io/oncoEnrichR/NA">
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+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script>
 </head>
 <body>
     <a href="https://sigven.github.io/oncoEnrichR/#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -31,7 +37,7 @@
     
     <a class="navbar-brand me-2" href="https://sigven.github.io/oncoEnrichR/index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 98a35e7..fb6fdfd 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -2,7 +2,13 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Contributor Code of Conduct • oncoEnrichR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Contributor Code of Conduct"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
@@ -10,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index de4352b..332e03e 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -2,7 +2,13 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • oncoEnrichR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
@@ -10,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/CHANGELOG.html b/articles/CHANGELOG.html
index 184f281..a60a548 100644
--- a/articles/CHANGELOG.html
+++ b/articles/CHANGELOG.html
@@ -23,7 +23,13 @@
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script>
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -33,7 +39,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -99,6 +105,43 @@
 
     
     
+<div class="section level2">
+<h2 id="version-1-4-2">Version 1.4.2<a class="anchor" aria-label="anchor" href="#version-1-4-2"></a>
+</h2>
+<ul>
+<li>Date: 2023-08-16</li>
+</ul>
+<div class="section level3">
+<h3 id="changed">Changed<a class="anchor" aria-label="anchor" href="#changed"></a>
+</h3>
+<ul>
+<li>Data updates
+<ul>
+<li>WikiPathways (20230810)</li>
+<li>COMPARTMENTS (2023-08)</li>
+<li>KEGG (20230710)</li>
+<li>BioGRID (v4.4.224)</li>
+<li>Open Targets Platform (2023.06)</li>
+<li>Upgraded <a href="https://github.com/sigven/phenOncoX" class="external-link">sigven/phenOncoX</a> to
+v0.6.3:
+<ul>
+<li>Experimental Factor Ontology (v3.56.0)</li>
+<li>Human Disease Ontology (2023-07-20)</li>
+</ul>
+</li>
+<li>A limited set of TCGA amplifications/deletions were erroneously left
+out in v1.4.1 (gene alias matching) - fixed in v1.4.2</li>
+</ul>
+</li>
+<li>Functionality
+<ul>
+<li>Updated <em>Citation Note</em> sections in report</li>
+<li>Fixed some typos in the report template</li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
 <div class="section level2">
 <h2 id="version-1-4-1">Version 1.4.1<a class="anchor" aria-label="anchor" href="#version-1-4-1"></a>
 </h2>
@@ -106,7 +149,7 @@ <h2 id="version-1-4-1">Version 1.4.1<a class="anchor" aria-label="anchor" href="
 <li>Date: 2023-06-18</li>
 </ul>
 <div class="section level3">
-<h3 id="changed">Changed<a class="anchor" aria-label="anchor" href="#changed"></a>
+<h3 id="changed-1">Changed<a class="anchor" aria-label="anchor" href="#changed-1"></a>
 </h3>
 <ul>
 <li>Data updates
@@ -148,7 +191,7 @@ <h2 id="version-1-4-0">Version 1.4.0<a class="anchor" aria-label="anchor" href="
 <li>Date: 2023-02-21</li>
 </ul>
 <div class="section level3">
-<h3 id="changed-1">Changed<a class="anchor" aria-label="anchor" href="#changed-1"></a>
+<h3 id="changed-2">Changed<a class="anchor" aria-label="anchor" href="#changed-2"></a>
 </h3>
 <ul>
 <li>Data updates
@@ -291,7 +334,7 @@ <h2 id="version-1-3-2">Version 1.3.2<a class="anchor" aria-label="anchor" href="
 <li>Date: 2022-09-27</li>
 </ul>
 <div class="section level3">
-<h3 id="changed-2">Changed<a class="anchor" aria-label="anchor" href="#changed-2"></a>
+<h3 id="changed-3">Changed<a class="anchor" aria-label="anchor" href="#changed-3"></a>
 </h3>
 <ul>
 <li>Cancer driver classification in <code>Cancer associations</code>
@@ -340,7 +383,7 @@ <h3 id="fixed">Fixed<a class="anchor" aria-label="anchor" href="#fixed"></a>
 </ul>
 </div>
 <div class="section level3">
-<h3 id="changed-3">Changed<a class="anchor" aria-label="anchor" href="#changed-3"></a>
+<h3 id="changed-4">Changed<a class="anchor" aria-label="anchor" href="#changed-4"></a>
 </h3>
 <ul>
 <li>Slight modification to column names in
@@ -368,7 +411,7 @@ <h3 id="added-1">Added<a class="anchor" aria-label="anchor" href="#added-1"></a>
 </ul>
 </div>
 <div class="section level3">
-<h3 id="changed-4">Changed<a class="anchor" aria-label="anchor" href="#changed-4"></a>
+<h3 id="changed-5">Changed<a class="anchor" aria-label="anchor" href="#changed-5"></a>
 </h3>
 <ul>
 <li>Fixed some artefacts (<code>-AS1</code> entries) in the output of
@@ -397,7 +440,7 @@ <h3 id="added-2">Added<a class="anchor" aria-label="anchor" href="#added-2"></a>
 </ul>
 </div>
 <div class="section level3">
-<h3 id="changed-5">Changed<a class="anchor" aria-label="anchor" href="#changed-5"></a>
+<h3 id="changed-6">Changed<a class="anchor" aria-label="anchor" href="#changed-6"></a>
 </h3>
 <ul>
 <li>Now using <a href="https://googledrive.tidyverse.org" class="external-link">googledrive</a> as data
@@ -432,7 +475,7 @@ <h2 id="version-1-2-0">Version 1.2.0<a class="anchor" aria-label="anchor" href="
 <li>Date: 2022-06-24</li>
 </ul>
 <div class="section level3">
-<h3 id="changed-6">Changed<a class="anchor" aria-label="anchor" href="#changed-6"></a>
+<h3 id="changed-7">Changed<a class="anchor" aria-label="anchor" href="#changed-7"></a>
 </h3>
 <ul>
 <li>Moved to <a href="https://doi.org/10.5281/zenodo.6684347" class="external-link">zenodo.org</a> for hosting
@@ -464,7 +507,7 @@ <h3 id="added-4">Added<a class="anchor" aria-label="anchor" href="#added-4"></a>
 </ul>
 </div>
 <div class="section level3">
-<h3 id="changed-7">Changed<a class="anchor" aria-label="anchor" href="#changed-7"></a>
+<h3 id="changed-8">Changed<a class="anchor" aria-label="anchor" href="#changed-8"></a>
 </h3>
 <ul>
 <li>Option renaming
@@ -536,7 +579,7 @@ <h3 id="added-5">Added<a class="anchor" aria-label="anchor" href="#added-5"></a>
 </ul>
 </div>
 <div class="section level3">
-<h3 id="changed-8">Changed<a class="anchor" aria-label="anchor" href="#changed-8"></a>
+<h3 id="changed-9">Changed<a class="anchor" aria-label="anchor" href="#changed-9"></a>
 </h3>
 <ul>
 <li>Re-ordering of HTML sections, multiple cosmetic changes</li>
@@ -595,7 +638,7 @@ <h3 id="fixed-3">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3"></a>
 </ul>
 </div>
 <div class="section level3">
-<h3 id="changed-9">Changed<a class="anchor" aria-label="anchor" href="#changed-9"></a>
+<h3 id="changed-10">Changed<a class="anchor" aria-label="anchor" href="#changed-10"></a>
 </h3>
 <ul>
 <li>Option <code>--show_crispr_lof</code> renamed to
@@ -648,7 +691,7 @@ <h3 id="added-7">Added<a class="anchor" aria-label="anchor" href="#added-7"></a>
 </ul>
 </div>
 <div class="section level3">
-<h3 id="changed-10">Changed<a class="anchor" aria-label="anchor" href="#changed-10"></a>
+<h3 id="changed-11">Changed<a class="anchor" aria-label="anchor" href="#changed-11"></a>
 </h3>
 <ul>
 <li>Refactoring of code and data for mapping gene identifiers</li>
@@ -681,7 +724,7 @@ <h3 id="added-8">Added<a class="anchor" aria-label="anchor" href="#added-8"></a>
 </ul>
 </div>
 <div class="section level3">
-<h3 id="changed-11">Changed<a class="anchor" aria-label="anchor" href="#changed-11"></a>
+<h3 id="changed-12">Changed<a class="anchor" aria-label="anchor" href="#changed-12"></a>
 </h3>
 <ul>
 <li>Management of annotation databases have been re-designed, reducing
diff --git a/articles/annotation_resources.html b/articles/annotation_resources.html
index c001770..c51ed23 100644
--- a/articles/annotation_resources.html
+++ b/articles/annotation_resources.html
@@ -23,7 +23,13 @@
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
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+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script>
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -33,7 +39,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,8 +117,8 @@ <h2 id="resources---overview">Resources - overview<a class="anchor" aria-label="
 associations</li>
 <li>
 <a href="http://bionlp.bcgsc.ca/cancermine/" class="external-link">CancerMine</a> -
-literature-mined database of drivers, oncogenes and tumor suppressors in
-cancer</li>
+literature-mined database of drivers, proto-oncogenes and tumor
+suppressors in cancer</li>
 <li>
 <a href="http://ncg.kcl.ac.uk/index.php" class="external-link">Network of Cancer Genes</a>
 - Network of cancer genes - a web resource to analyze duplicability,
@@ -120,7 +126,9 @@ <h2 id="resources---overview">Resources - overview<a class="anchor" aria-label="
 <li>
 <a href="https://www.intogen.org" class="external-link">IntOGen</a> - Compendium of
 mutational driver genes in cancer</li>
-<li><a href="https://uniprot.org" class="external-link">UniProt</a></li>
+<li>
+<a href="https://uniprot.org" class="external-link">UniProt</a> - Comprehensive and freely
+accessible resource of protein sequence and functional information</li>
 <li><a href="https://cancer.sanger.ac.uk/census" class="external-link">Cancer Gene
 Census</a></li>
 <li>
@@ -373,12 +381,13 @@ <h3 id="celltissue-specific-gene-expression-patterns">Cell/tissue-specific gene
 annotations from the <a href="https://proteinatlas.org" class="external-link">Human Protein
 Atlas</a>. Tissue-specific patterns are derived from <a href="https://www.proteinatlas.org/humanproteome/tissue" class="external-link">The Tissue
 Atlas</a>, where tissue specificity is derived from deep sequencing of
-RNA (RNA-seq) in 54 different normal tissue types. All putative
+RNA (RNA-seq) in 50 different normal tissue types. All putative
 protein-coding genes have been classified with respect to abundance
 (tissue enriched, tissue enhanced etc.) for different tissues. For cell
-type specificity, we utilize data from <a href="https://www.proteinatlas.org/humanproteome/celltype" class="external-link">The Cell Type
-Atlas</a>. Here, classification of all protein-coding genes based on
-single cell type-specific expression in 79 different cell types are
+type specificity, we utilize <a href="https://www.proteinatlas.org/about/assays+annotation#singlecell_rna" class="external-link">single
+cell RNA (scRNA) sequencing datasets</a> aggregated within the Human
+Protein Atlas. Here, classification of all protein-coding genes based on
+single cell type-specific expression in 81 different cell types are
 performed; determining the types of genes elevated (cell type enriched,
 cell type enhanced etc.) in a particular cell type compared to all other
 cell types.</li>
diff --git a/articles/cancer_gene_rank.html b/articles/cancer_gene_rank.html
index fb083e7..b6545fa 100644
--- a/articles/cancer_gene_rank.html
+++ b/articles/cancer_gene_rank.html
@@ -23,7 +23,13 @@
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script>
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -33,7 +39,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index 37a5180..8bf9b7b 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -2,7 +2,13 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • oncoEnrichR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
@@ -10,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/input.html b/articles/input.html
index 24ef971..54593ae 100644
--- a/articles/input.html
+++ b/articles/input.html
@@ -23,7 +23,13 @@
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script>
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -33,7 +39,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/installation.html b/articles/installation.html
index 3c80031..e04a6b5 100644
--- a/articles/installation.html
+++ b/articles/installation.html
@@ -23,7 +23,13 @@
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script>
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -33,7 +39,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -104,15 +110,15 @@ <h2 id="requirementsdependencies">Requirements/dependencies<a class="anchor" ari
 </h2>
 <ul>
 <li>
-<em>oncoEnrichR</em> requires R (&gt;=4.1)</li>
+<em>oncoEnrichR</em> requires R (&gt;= version 4.1)</li>
 </ul>
 </div>
 <div class="section level2">
 <h2 id="installation-of-oncoenrichr-with-r-commands">Installation of oncoEnrichR with R commands<a class="anchor" aria-label="anchor" href="#installation-of-oncoenrichr-with-r-commands"></a>
 </h2>
 <ol style="list-style-type: decimal">
-<li><code>install.packages('devtools')</code></li>
-<li><code>devtools::install_github('sigven/oncoEnrichR', ref = "v1.4.1")</code></li>
+<li><code>install.packages('remotes')</code></li>
+<li><code>remotes::install_github('sigven/oncoEnrichR', ref = "v1.4.2")</code></li>
 <li><code><a href="https://github.com/sigven/oncoEnrichR" class="external-link">library(oncoEnrichR)</a></code></li>
 </ol>
 <p><br></p>
diff --git a/articles/output.html b/articles/output.html
index f191098..0498b5d 100644
--- a/articles/output.html
+++ b/articles/output.html
@@ -23,7 +23,13 @@
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+  gtag('config', 'G-N4MB4571K5');
+</script>
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -33,7 +39,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/running.html b/articles/running.html
index 1d26265..8511355 100644
--- a/articles/running.html
+++ b/articles/running.html
@@ -23,7 +23,13 @@
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script>
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -33,7 +39,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 6b06e55..3263f21 100644
--- a/authors.html
+++ b/authors.html
@@ -2,7 +2,13 @@
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@@ -10,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
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@@ -74,15 +80,14 @@ <h2>Authors</h2>
       <h2 id="citation">Citation</h2>
       <p><small class="dont-index">Source: <a href="https://github.com/sigven/oncoEnrichR/blob/HEAD/inst/CITATION" class="external-link"><code>inst/CITATION</code></a></small></p>
 
-      <p>Sigve Nakken, Sveinung Gundersen, Fabian L. M. Bernal, Eivind Hovig, and Jørgen Wesche. OncoEnrichR: cancer-dedicated gene set interpretation (2021). arXiv:2107.13247v2. https://arxiv.org/abs/2107.13247v2</p>
-      <pre>@Misc{,
-  title = {oncoEnrichR: cancer-dedicated gene set interpretation},
-  author = {Sigve Nakken and Sveinung Gundersen and Fabian L. M. Bernal and Eivind Hovig and Jørgen Wesche},
-  year = {2021},
-  eprint = {2107.13247v2},
-  archiveprefix = {arXiv},
-  primaryclass = {q-bio.GN},
-  url = {https://arxiv.org/abs/2107.13247v2},
+      <p>Sigve Nakken, Sveinung Gundersen, Fabian L. M. Bernal, Dimitris Polychronopoulos, Eivind Hovig, and Jørgen Wesche. Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR (2023). Int J Cancer. https://doi.org/10.1002/ijc.34666</p>
+      <pre>@Article{,
+  title = {Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR},
+  author = {Sigve Nakken and Sveinung Gundersen and Fabian L. M. Bernal and Dimitris Polychronopoulos and Eivind Hovig and Jørgen Wesche},
+  year = {2023},
+  doi = {10.1002/ijc.34666},
+  url = {https://doi.org/10.1002/ijc.34666},
+  journal = {Int. J. Cancer},
 }</pre>
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transparent;--bs-gradient: none}.btn-outline-light{--bs-btn-color: #f8f9fa;--bs-btn-border-color: #f8f9fa;--bs-btn-hover-color: #000;--bs-btn-hover-bg: #f8f9fa;--bs-btn-hover-border-color: #f8f9fa;--bs-btn-focus-shadow-rgb: 248,249,250;--bs-btn-active-color: #000;--bs-btn-active-bg: #f8f9fa;--bs-btn-active-border-color: #f8f9fa;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #f8f9fa;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #f8f9fa;--bs-btn-bg: transparent;--bs-gradient: none}.btn-outline-dark{--bs-btn-color: #212529;--bs-btn-border-color: #212529;--bs-btn-hover-color: #fff;--bs-btn-hover-bg: #212529;--bs-btn-hover-border-color: #212529;--bs-btn-focus-shadow-rgb: 33,37,41;--bs-btn-active-color: #fff;--bs-btn-active-bg: #212529;--bs-btn-active-border-color: #212529;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #212529;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #212529;--bs-btn-bg: transparent;--bs-gradient: none}.btn-link{--bs-btn-font-weight: 400;--bs-btn-color: var(--bs-link-color);--bs-btn-bg: transparent;--bs-btn-border-color: transparent;--bs-btn-hover-color: var(--bs-link-hover-color);--bs-btn-hover-border-color: transparent;--bs-btn-active-color: var(--bs-link-hover-color);--bs-btn-active-border-color: transparent;--bs-btn-disabled-color: #6c757d;--bs-btn-disabled-border-color: transparent;--bs-btn-box-shadow: none;--bs-btn-focus-shadow-rgb: 49,132,253;text-decoration:underline;-webkit-text-decoration:underline;-moz-text-decoration:underline;-ms-text-decoration:underline;-o-text-decoration:underline}.btn-link:focus-visible{color:var(--bs-btn-color)}.btn-link:hover{color:var(--bs-btn-hover-color)}.btn-lg,.btn-group-lg>.btn{--bs-btn-padding-y: .5rem;--bs-btn-padding-x: 1rem;--bs-btn-font-size:1.25rem;--bs-btn-border-radius: .5rem}.btn-sm,.btn-group-sm>.btn{--bs-btn-padding-y: .25rem;--bs-btn-padding-x: 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auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:.375rem}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:-1px}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n + 3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:-1px}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: #6c757d;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link.disabled{color:var(--bs-nav-link-disabled-color);pointer-events:none;cursor:default}.nav-tabs{--bs-nav-tabs-border-width: 1px;--bs-nav-tabs-border-color: #dee2e6;--bs-nav-tabs-border-radius: .375rem;--bs-nav-tabs-link-hover-border-color: #e9ecef #e9ecef #dee2e6;--bs-nav-tabs-link-active-color: #495057;--bs-nav-tabs-link-active-bg: #fff;--bs-nav-tabs-link-active-border-color: #dee2e6 #dee2e6 #fff;border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));background:none;border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.disabled,.nav-tabs .nav-link:disabled{color:var(--bs-nav-link-disabled-color);background-color:transparent;border-color:transparent}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show 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992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas 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.offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse,.bslib-sidebar-layout>.sidebar>.sidebar-content>.accordion .accordion-collapse{border-width:0}.accordion-flush .accordion-item,.bslib-sidebar-layout>.sidebar>.sidebar-content>.accordion .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child,.bslib-sidebar-layout>.sidebar>.sidebar-content>.accordion .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child,.bslib-sidebar-layout>.sidebar>.sidebar-content>.accordion .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.bslib-sidebar-layout>.sidebar>.sidebar-content>.accordion .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: #6c757d;--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: #6c757d;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: 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1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 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.25em;color:#000;background:transparent url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e") center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:.5}.btn-close:hover{color:#000;text-decoration:none;opacity:.75}.btn-close:focus{outline:0;box-shadow:0 0 0 .25rem rgba(13,110,253,0.25);opacity:1}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:.25}.btn-close-white{filter:invert(1) grayscale(100%) brightness(200%)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 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transparent;--bs-gradient: none}.btn-outline-light{--bs-btn-color: #f8f9fa;--bs-btn-border-color: #f8f9fa;--bs-btn-hover-color: #000;--bs-btn-hover-bg: #f8f9fa;--bs-btn-hover-border-color: #f8f9fa;--bs-btn-focus-shadow-rgb: 248,249,250;--bs-btn-active-color: #000;--bs-btn-active-bg: #f8f9fa;--bs-btn-active-border-color: #f8f9fa;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #f8f9fa;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #f8f9fa;--bs-btn-bg: transparent;--bs-gradient: none}.btn-outline-dark{--bs-btn-color: #212529;--bs-btn-border-color: #212529;--bs-btn-hover-color: #fff;--bs-btn-hover-bg: #212529;--bs-btn-hover-border-color: #212529;--bs-btn-focus-shadow-rgb: 33,37,41;--bs-btn-active-color: #fff;--bs-btn-active-bg: #212529;--bs-btn-active-border-color: #212529;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #212529;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #212529;--bs-btn-bg: transparent;--bs-gradient: none}.btn-link{--bs-btn-font-weight: 400;--bs-btn-color: var(--bs-link-color);--bs-btn-bg: transparent;--bs-btn-border-color: transparent;--bs-btn-hover-color: var(--bs-link-hover-color);--bs-btn-hover-border-color: transparent;--bs-btn-active-color: var(--bs-link-hover-color);--bs-btn-active-border-color: transparent;--bs-btn-disabled-color: #6c757d;--bs-btn-disabled-border-color: transparent;--bs-btn-box-shadow: none;--bs-btn-focus-shadow-rgb: 49,132,253;text-decoration:underline;-webkit-text-decoration:underline;-moz-text-decoration:underline;-ms-text-decoration:underline;-o-text-decoration:underline}.btn-link:focus-visible{color:var(--bs-btn-color)}.btn-link:hover{color:var(--bs-btn-hover-color)}.btn-lg,.btn-group-lg>.btn{--bs-btn-padding-y: .5rem;--bs-btn-padding-x: 1rem;--bs-btn-font-size:1.25rem;--bs-btn-border-radius: .5rem}.btn-sm,.btn-group-sm>.btn{--bs-btn-padding-y: .25rem;--bs-btn-padding-x: 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10rem;--bs-dropdown-padding-x: 0;--bs-dropdown-padding-y: .5rem;--bs-dropdown-spacer: .125rem;--bs-dropdown-font-size:1rem;--bs-dropdown-color: #212529;--bs-dropdown-bg: #fff;--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-border-radius: .375rem;--bs-dropdown-border-width: 1px;--bs-dropdown-inner-border-radius: calc(.375rem - 1px);--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-divider-margin-y: .5rem;--bs-dropdown-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15);--bs-dropdown-link-color: #212529;--bs-dropdown-link-hover-color: #1e2125;--bs-dropdown-link-hover-bg: #e9ecef;--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #0d6efd;--bs-dropdown-link-disabled-color: #adb5bd;--bs-dropdown-item-padding-x: 1rem;--bs-dropdown-item-padding-y: .25rem;--bs-dropdown-header-color: #6c757d;--bs-dropdown-header-padding-x: 1rem;--bs-dropdown-header-padding-y: .5rem;position:absolute;z-index:var(--bs-dropdown-zindex);display:none;min-width:var(--bs-dropdown-min-width);padding:var(--bs-dropdown-padding-y) var(--bs-dropdown-padding-x);margin:0;font-size:var(--bs-dropdown-font-size);color:var(--bs-dropdown-color);text-align:left;list-style:none;background-color:var(--bs-dropdown-bg);background-clip:padding-box;border:var(--bs-dropdown-border-width) solid var(--bs-dropdown-border-color);border-radius:var(--bs-dropdown-border-radius)}.dropdown-menu[data-bs-popper]{top:100%;left:0;margin-top:var(--bs-dropdown-spacer)}.dropdown-menu-start{--bs-position: start}.dropdown-menu-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-end{--bs-position: end}.dropdown-menu-end[data-bs-popper]{right:0;left:auto}@media (min-width: 576px){.dropdown-menu-sm-start{--bs-position: start}.dropdown-menu-sm-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-sm-end{--bs-position: end}.dropdown-menu-sm-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 768px){.dropdown-menu-md-start{--bs-position: start}.dropdown-menu-md-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-md-end{--bs-position: end}.dropdown-menu-md-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 992px){.dropdown-menu-lg-start{--bs-position: start}.dropdown-menu-lg-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-lg-end{--bs-position: end}.dropdown-menu-lg-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 1200px){.dropdown-menu-xl-start{--bs-position: start}.dropdown-menu-xl-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-xl-end{--bs-position: end}.dropdown-menu-xl-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 1400px){.dropdown-menu-xxl-start{--bs-position: start}.dropdown-menu-xxl-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-xxl-end{--bs-position: end}.dropdown-menu-xxl-end[data-bs-popper]{right:0;left:auto}}.dropup .dropdown-menu[data-bs-popper]{top:auto;bottom:100%;margin-top:0;margin-bottom:var(--bs-dropdown-spacer)}.dropup .dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:"";border-top:0;border-right:.3em solid transparent;border-bottom:.3em solid;border-left:.3em solid transparent}.dropup .dropdown-toggle:empty::after{margin-left:0}.dropend .dropdown-menu[data-bs-popper]{top:0;right:auto;left:100%;margin-top:0;margin-left:var(--bs-dropdown-spacer)}.dropend .dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:"";border-top:.3em solid transparent;border-right:0;border-bottom:.3em solid transparent;border-left:.3em solid}.dropend .dropdown-toggle:empty::after{margin-left:0}.dropend .dropdown-toggle::after{vertical-align:0}.dropstart .dropdown-menu[data-bs-popper]{top:0;right:100%;left:auto;margin-top:0;margin-right:var(--bs-dropdown-spacer)}.dropstart .dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:""}.dropstart .dropdown-toggle::after{display:none}.dropstart .dropdown-toggle::before{display:inline-block;margin-right:.255em;vertical-align:.255em;content:"";border-top:.3em solid transparent;border-right:.3em solid;border-bottom:.3em solid transparent}.dropstart .dropdown-toggle:empty::after{margin-left:0}.dropstart .dropdown-toggle::before{vertical-align:0}.dropdown-divider{height:0;margin:var(--bs-dropdown-divider-margin-y) 0;overflow:hidden;border-top:1px solid var(--bs-dropdown-divider-bg);opacity:1}.dropdown-item{display:block;width:100%;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);clear:both;font-weight:400;color:var(--bs-dropdown-link-color);text-align:inherit;text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;white-space:nowrap;background-color:transparent;border:0}.dropdown-item:hover,.dropdown-item:focus{color:var(--bs-dropdown-link-hover-color);background-color:var(--bs-dropdown-link-hover-bg)}.dropdown-item.active,.dropdown-item:active{color:var(--bs-dropdown-link-active-color);text-decoration:none;background-color:var(--bs-dropdown-link-active-bg)}.dropdown-item.disabled,.dropdown-item:disabled{color:var(--bs-dropdown-link-disabled-color);pointer-events:none;background-color:transparent}.dropdown-menu.show{display:block}.dropdown-header{display:block;padding:var(--bs-dropdown-header-padding-y) var(--bs-dropdown-header-padding-x);margin-bottom:0;font-size:.875rem;color:var(--bs-dropdown-header-color);white-space:nowrap}.dropdown-item-text{display:block;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);color:var(--bs-dropdown-link-color)}.dropdown-menu-dark{--bs-dropdown-color: #dee2e6;--bs-dropdown-bg: #343a40;--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-box-shadow: ;--bs-dropdown-link-color: #dee2e6;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #0d6efd;--bs-dropdown-link-disabled-color: #adb5bd;--bs-dropdown-header-color: #adb5bd}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:.375rem}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:-1px}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n + 3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:-1px}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: #6c757d;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link.disabled{color:var(--bs-nav-link-disabled-color);pointer-events:none;cursor:default}.nav-tabs{--bs-nav-tabs-border-width: 1px;--bs-nav-tabs-border-color: #dee2e6;--bs-nav-tabs-border-radius: .375rem;--bs-nav-tabs-link-hover-border-color: #e9ecef #e9ecef #dee2e6;--bs-nav-tabs-link-active-color: #495057;--bs-nav-tabs-link-active-bg: #fff;--bs-nav-tabs-link-active-border-color: #dee2e6 #dee2e6 #fff;border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));background:none;border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.disabled,.nav-tabs .nav-link:disabled{color:var(--bs-nav-link-disabled-color);background-color:transparent;border-color:transparent}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * var(--bs-nav-tabs-border-width));border-top-left-radius:0;border-top-right-radius:0}.nav-pills{--bs-nav-pills-border-radius: .375rem;--bs-nav-pills-link-active-color: #fff;--bs-nav-pills-link-active-bg: #0d6efd}.nav-pills .nav-link{background:none;border:0;border-radius:var(--bs-nav-pills-border-radius)}.nav-pills .nav-link:disabled{color:var(--bs-nav-link-disabled-color);background-color:transparent;border-color:transparent}.nav-pills .nav-link.active,.nav-pills .show>.nav-link{color:var(--bs-nav-pills-link-active-color);background-color:var(--bs-nav-pills-link-active-bg)}.nav-fill>.nav-link,.nav-fill .nav-item{flex:1 1 auto;-webkit-flex:1 1 auto;text-align:center}.nav-justified>.nav-link,.nav-justified 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.offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: #6c757d;--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: #6c757d;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: #fff;--bs-pagination-border-width: 1px;--bs-pagination-border-color: #dee2e6;--bs-pagination-border-radius: .375rem;--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: #e9ecef;--bs-pagination-hover-border-color: #dee2e6;--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: #e9ecef;--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(13,110,253,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #0d6efd;--bs-pagination-active-border-color: #0d6efd;--bs-pagination-disabled-color: #6c757d;--bs-pagination-disabled-bg: #fff;--bs-pagination-disabled-border-color: #dee2e6;display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 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.page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: .5rem}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: .25rem}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: .375rem;display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: 1px solid var(--bs-alert-border-color);--bs-alert-border-radius: .375rem;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: #595a5c;--bs-alert-bg: #f8f9fa;--bs-alert-border-color: #f5f6f8}.alert-default .alert-link{color:#47484a}.alert-primary{--bs-alert-color: #084298;--bs-alert-bg: #cfe2ff;--bs-alert-border-color: #b6d4fe}.alert-primary .alert-link{color:#06357a}.alert-secondary{--bs-alert-color: #41464b;--bs-alert-bg: #e2e3e5;--bs-alert-border-color: #d3d6d8}.alert-secondary .alert-link{color:#34383c}.alert-success{--bs-alert-color: #0f5132;--bs-alert-bg: #d1e7dd;--bs-alert-border-color: #badbcc}.alert-success .alert-link{color:#0c4128}.alert-info{--bs-alert-color: #055160;--bs-alert-bg: #cff4fc;--bs-alert-border-color: #b6effb}.alert-info .alert-link{color:#04414d}.alert-warning{--bs-alert-color: #664d03;--bs-alert-bg: #fff3cd;--bs-alert-border-color: #ffecb5}.alert-warning .alert-link{color:#523e02}.alert-danger{--bs-alert-color: #842029;--bs-alert-bg: #f8d7da;--bs-alert-border-color: #f5c2c7}.alert-danger .alert-link{color:#6a1a21}.alert-light{--bs-alert-color: #636464;--bs-alert-bg: #fefefe;--bs-alert-border-color: #fdfdfe}.alert-light .alert-link{color:#4f5050}.alert-dark{--bs-alert-color: #141619;--bs-alert-bg: #d3d3d4;--bs-alert-border-color: #bcbebf}.alert-dark .alert-link{color:#101214}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: #e9ecef;--bs-progress-border-radius: .375rem;--bs-progress-box-shadow: inset 0 1px 2px rgba(0,0,0,0.075);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #0d6efd;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: #212529;--bs-list-group-bg: #fff;--bs-list-group-border-color: rgba(0,0,0,0.125);--bs-list-group-border-width: 1px;--bs-list-group-border-radius: .375rem;--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: #495057;--bs-list-group-action-hover-color: #495057;--bs-list-group-action-hover-bg: #f8f9fa;--bs-list-group-action-active-color: #212529;--bs-list-group-action-active-bg: #e9ecef;--bs-list-group-disabled-color: #6c757d;--bs-list-group-disabled-bg: #fff;--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #0d6efd;--bs-list-group-active-border-color: #0d6efd;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid 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diff --git a/index.html b/index.html
index ecff622..13c8c6e 100644
--- a/index.html
+++ b/index.html
@@ -55,7 +55,13 @@
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
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+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script>
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -65,7 +71,7 @@
     
     <a class="navbar-brand me-2" href="index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -126,7 +132,7 @@
 </div>
 <p><strong>oncoEnrichR</strong> is an R package for functional interrogation of human genesets in the context of cancer. It is primarily intended for exploratory analysis, interpretation, and prioritization of long gene lists, which represent a common output from many types of high-throughput cancer biology screens.</p>
 <p><strong>oncoEnrichR</strong> can be used to interrogate results from e.g. genetic screens (siRNA/CRISPR), protein proximity labeling, or transcriptomics (differential expression). The tool queries a variety of high-quality data resources in order to assemble useful gene annotations and analyses in an interactive report (examples from the report shown below).</p>
-<p>Web-based access to <strong>oncoEnrichR</strong> is available at <font size="4"> <a href="https://oncotools.elixir.no/tool_runner?tool_id=galaxy-ntnu.bioinfo.no%2Ftoolshed_nels%2Frepos%2Fradmilko%2Foncoenrichr%2Foncoenrichr_wrapper%2F1.4.1" class="external-link"><strong>https://oncotools.elixir.no</strong></a></font></p>
+<p>Web-based access to <strong>oncoEnrichR</strong> is available at <font size="4"> <a href="https://oncotools.elixir.no/tool_runner?tool_id=galaxy-ntnu.bioinfo.no%2Ftoolshed_nels%2Frepos%2Fradmilko%2Foncoenrichr%2Foncoenrichr_wrapper%2F1.4.2" class="external-link"><strong>https://oncotools.elixir.no</strong></a></font></p>
 <p><br></p>
 <p><img src="reference/figures/oncoenrichr_overview.png" align="center" border="0"></p>
 <p><br><br></p>
@@ -158,6 +164,8 @@ <h2 id="questions-addressed-by-oncoenrichr">Questions addressed by oncoEnrichR<a
 <h2 id="news">News<a class="anchor" aria-label="anchor" href="#news"></a>
 </h2>
 <ul>
+<li>August 16th 2023: <a href="articles/CHANGELOG.html#version-1-4-2"><strong>1.4.2 release</strong></a>
+</li>
 <li>June 18th 2023: <a href="articles/CHANGELOG.html#version-1-4-1"><strong>1.4.1 release</strong></a>
 </li>
 <li>February 21st 2023: <a href="articles/CHANGELOG.html#version-1-4-0"><strong>1.4.0 release</strong></a>
@@ -167,9 +175,15 @@ <h2 id="news">News<a class="anchor" aria-label="anchor" href="#news"></a>
 </ul>
 </div>
 <div class="section level2">
+<h2 id="citation">Citation<a class="anchor" aria-label="anchor" href="#citation"></a>
+</h2>
+<p>If you use oncoEnrichR, please cite the following publication:</p>
+<p>Sigve Nakken, Sveinung Gundersen, Fabian L. M. Bernal, Dimitris Polychronopoulos, Eivind Hovig, and Jørgen Wesche. <strong>Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR</strong> (2023). Int J Cancer. <a href="https://doi.org/10.1002/ijc.34666" class="external-link">doi:10.1002/ijc.34666</a></p>
+</div>
+<div class="section level2">
 <h2 id="example-report">Example report<a class="anchor" aria-label="anchor" href="#example-report"></a>
 </h2>
-<p><a href="https://doi.org/10.5281/zenodo.8051153" class="external-link"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.8051153.svg" alt="DOI"></a></p>
+<p><a href="https://doi.org/10.5281/zenodo.8247877" class="external-link"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.8247877.svg" alt="DOI"></a></p>
 <p><br></p>
 </div>
 <div class="section level2">
diff --git a/pkgdown.yml b/pkgdown.yml
index b5230d8..fa04d68 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -9,7 +9,7 @@ articles:
   installation: installation.html
   output: output.html
   running: running.html
-last_built: 2023-06-17T22:57Z
+last_built: 2023-08-16T10:26Z
 urls:
   reference: https://sigven.github.io/oncoEnrichR/reference
   article: https://sigven.github.io/oncoEnrichR/articles
diff --git a/reference/gseabase.html b/reference/gseabase.html
index 509811b..904d992 100644
--- a/reference/gseabase.html
+++ b/reference/gseabase.html
@@ -2,7 +2,13 @@
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
@@ -10,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 1aa11e0..b7a3739 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -2,7 +2,13 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function reference • oncoEnrichR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
@@ -10,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/init_report.html b/reference/init_report.html
index 618d916..58b3ea8 100644
--- a/reference/init_report.html
+++ b/reference/init_report.html
@@ -1,8 +1,14 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Load oncoEnrichR annotation database"><title>Load oncoEnrichR annotation database — init_report • oncoEnrichR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Load oncoEnrichR annotation database — init_report"><meta property="og:description" content="Load oncoEnrichR annotation database"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Function that initiates oncoEnrichR report structure"><title>Function that initiates oncoEnrichR report structure — init_report • oncoEnrichR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function that initiates oncoEnrichR report structure — init_report"><meta property="og:description" content="Function that initiates oncoEnrichR report structure"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
@@ -10,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -58,13 +64,13 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Load oncoEnrichR annotation database</h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Function that initiates oncoEnrichR report structure</h1>
       <small class="dont-index">Source: <a href="https://github.com/sigven/oncoEnrichR/blob/HEAD/R/onco_enrichr.R" class="external-link"><code>R/onco_enrichr.R</code></a></small>
       <div class="d-none name"><code>init_report.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>Load oncoEnrichR annotation database</p>
+    <p>Function that initiates oncoEnrichR report structure</p>
     </div>
 
     <div class="section level2">
@@ -312,14 +318,6 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dt>show_domain</dt>
 <dd><p>logical indicating if report should provide target memberships in known protein domains (Pfam)</p></dd>
 
-
-<dt>remote</dt>
-<dd><p>If TRUE (default), load database from version-tagged Zenodo repository</p></dd>
-
-
-<dt>cache_dir</dt>
-<dd><p>path to local cache for more efficient subsequent loads</p></dd>
-
 </dl></div>
 
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/load_db.html b/reference/load_db.html
index bafebbd..7ec75af 100644
--- a/reference/load_db.html
+++ b/reference/load_db.html
@@ -4,7 +4,13 @@
 repository from Google Drive"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
@@ -12,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/onco_enrich.html b/reference/onco_enrich.html
index b679cdb..9b2be70 100644
--- a/reference/onco_enrich.html
+++ b/reference/onco_enrich.html
@@ -12,7 +12,13 @@
 synthetic lethality interactions, prognostic associations, and more."><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
@@ -20,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/tidyeval.html b/reference/tidyeval.html
index a7d50d7..06ecd19 100644
--- a/reference/tidyeval.html
+++ b/reference/tidyeval.html
@@ -2,7 +2,13 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html"><title>Tidy eval helpers — tidyeval • oncoEnrichR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Tidy eval helpers — tidyeval"><meta property="og:description" content="https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
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diff --git a/reference/url_exists.html b/reference/url_exists.html
deleted file mode 100644
index ddae89f..0000000
--- a/reference/url_exists.html
+++ /dev/null
@@ -1,90 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="RCurl url.exists"><title>RCurl url.exists — url_exists • oncoEnrichR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RCurl url.exists — url_exists"><meta property="og:description" content="RCurl url.exists"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
-    
-    <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
-
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
-
-    
-    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
-      <span class="navbar-toggler-icon"></span>
-    </button>
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-    <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../index.html">Intro</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../articles/installation.html">Installation</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../articles/running.html">Running</a>
-</li>
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-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-    <a class="dropdown-item" href="../articles/input.html">Input</a>
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-    <a class="dropdown-item" href="../articles/annotation_resources.html">Annotation resources</a>
-    <a class="dropdown-item" href="../articles/cancer_gene_rank.html">Cancer gene rank</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../articles/CHANGELOG.html">CHANGELOG</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-  </div>
-</nav><div class="container template-reference-topic">
-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>RCurl url.exists</h1>
-      <small class="dont-index">Source: <a href="https://github.com/sigven/oncoEnrichR/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
-      <div class="d-none name"><code>url_exists.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p>RCurl url.exists</p>
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-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by <a href="https://github.com/sigven" class="external-link">Sigve Nakken</a>.</p>
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diff --git a/reference/validate_db.html b/reference/validate_db.html
index 23844b0..654d7cb 100644
--- a/reference/validate_db.html
+++ b/reference/validate_db.html
@@ -2,7 +2,13 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Function that validates the oncoEnrichR database object"><title>Function that validates the oncoEnrichR database object — validate_db • oncoEnrichR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function that validates the oncoEnrichR database object — validate_db"><meta property="og:description" content="Function that validates the oncoEnrichR database object"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--></head><body>
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
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+  gtag('js', new Date());
+
+  gtag('config', 'G-N4MB4571K5');
+</script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
@@ -10,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/validate_db_df.html b/reference/validate_db_df.html
index 6e61bf6..531760b 100644
--- a/reference/validate_db_df.html
+++ b/reference/validate_db_df.html
@@ -2,7 +2,13 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Function that validates a particular db object (data.frame) in oncoEnrichR"><title>Function that validates a particular db object (data.frame) in oncoEnrichR — validate_db_df • oncoEnrichR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function that validates a particular db object (data.frame) in oncoEnrichR — validate_db_df"><meta property="og:description" content="Function that validates a particular db object (data.frame) in oncoEnrichR"><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--></head><body>
+<![endif]--><script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script><script>
+  window.dataLayer = window.dataLayer || [];
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+  gtag('config', 'G-N4MB4571K5');
+</script></head><body>
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@@ -10,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
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diff --git a/reference/write.html b/reference/write.html
index edb2ae1..2a80e2d 100644
--- a/reference/write.html
+++ b/reference/write.html
@@ -4,7 +4,13 @@
 either as an interactive HTML report or as an Excel workbook."><meta property="og:image" content="https://sigven.github.io/oncoEnrichR/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">oncoEnrichR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.4.2</small>
 
     
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diff --git a/search.json b/search.json
index 9e4b37d..af77e3e 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://sigven.github.io/oncoEnrichR/CODE_OF_CONDUCT.html","id":null,"dir":"","previous_headings":"","what":"Contributor Code of Conduct","title":"Contributor Code of Conduct","text":"contributors maintainers project, pledge respect people contribute reporting issues, posting feature requests, updating documentation, submitting pull requests patches, activities. committed making participation project harassment-free experience everyone, regardless level experience, gender, gender identity expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, religion. Examples unacceptable behavior participants include use sexual language imagery, derogatory comments personal attacks, trolling, public private harassment, insults, unprofessional conduct. Project maintainers right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct. Project maintainers follow Code Conduct may removed project team. Instances abusive, harassing, otherwise unacceptable behavior may reported opening issue contacting one project maintainers. 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show_coexpression","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"fixed-1","dir":"Articles","previous_headings":"Version 1.1.1","what":"Fixed","title":"Changelog","text":"Bug: database loading missing pfamdb Relaxed dependency versions (caused conflicts R versions < 4.2)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-1-0","dir":"Articles","previous_headings":"","what":"Version 1.1.0","title":"Changelog","text":"Date: 2022-06-10","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-5","dir":"Articles","previous_headings":"Version 1.1.0","what":"Added","title":"Changelog","text":"CancerMine (v46) Open Targets Platform (2022.04) WikiPathways (20220510) GENCODE (v40) CGC (v96) TCGA (GDC release 32) EFO (v42.0) Module shows occurrence protein domains among query set members Protein-complex cancer relevance score ppi_node_shadow - logical indicating nodes PPI 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1.0.9","what":"Changed","title":"Changelog","text":"Option --show_crispr_lof renamed --show_fitness. Corresponding section HTML report renamed CRISPR/Cas9 loss--fitness Gene fitness scores. TCGA co-expression –> Tumor co-expression TCGA aberration frequency —> Tumor aberration frequencies TCGA prognostic associations —> Prognostic associations Sections include tabsets now organized initial active tab always contains data (exception tabs empty)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-0-8","dir":"Articles","previous_headings":"","what":"Version 1.0.8","title":"Changelog","text":"Date: 2022-02-18","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-7","dir":"Articles","previous_headings":"Version 1.0.8","what":"Added","title":"Changelog","text":"WikiPathways (20220210) CancerMine (v42) MSigDB (v7.5.1) GENCODE (v39) Gene summary (NCBI) Reactome/GO (MSigDB v7.5.1) KEGG (20211223)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-10","dir":"Articles","previous_headings":"Version 1.0.8","what":"Changed","title":"Changelog","text":"Refactoring code data mapping gene identifiers Refactoring code database loading","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-0-7","dir":"Articles","previous_headings":"","what":"Version 1.0.7","title":"Changelog","text":"Date: 2021-11-30","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-8","dir":"Articles","previous_headings":"Version 1.0.7","what":"Added","title":"Changelog","text":"WikiPathways (20211110) Open Targets Platform (2021.11) EFO (v3.36.0) TCGA (v31, 2021-10-29) CancerMine (v40) Human Protein Atlas (v21) UniProt KB (2021_04) PFAM domains (release 35, November 2021)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-11","dir":"Articles","previous_headings":"Version 1.0.7","what":"Changed","title":"Changelog","text":"Management annotation databases re-designed, reducing size installation oncoEnrichR significantly. re-design results addition initial step analysis; database loading.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-0-6","dir":"Articles","previous_headings":"","what":"Version 1.0.6","title":"Changelog","text":"Date: 2021-10-27","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-9","dir":"Articles","previous_headings":"Version 1.0.6","what":"Added","title":"Changelog","text":"KEGG (20211013) WikiPathways (20211010) Open Targets Platform (2021.09) EFO (v3.35.0), DiseaseOntology (v2021-10-11) TCGA (v30, 2021-09-23) Protein complex annotations - additions Compleat, ComplexPortal, PDB, hu.MAP2 View overlap members queryset previously established regulatory interactions (TF-target relationships) DoRothEA resource Explore potential ligand-receptor interactions query set, found CellChat database Choose Bootswatch theme HTML report - option html_report_theme Choose table contents placed HTML report (floating-left static top) - option html_floating_toc html_floating_toc - logical, set FALSE, table contents HTML report placed top main document html_report_theme - character, choose different Bootswatch themes style HTML report show_regulatory - logical, show regulatory interactions module (DoRothEA) min_confidence_reg_interaction - character, minimum confidence regulatory interactions included DoRothEA (‘’,‘B’,‘C’, ‘D’) show_ligand_receptor - logical, show ligand-receptor interaction module (CellChatDB) num_terms_enrichment_plot - integer, number enriched Gene Ontology terms (max) show enrichment barplots (module Functional Enrichment) modules Regulatory Interactions Tissue cell type enrichment, interactions/targets ranked according quantitative cancer association score cancer_max_rank (maximum gene-cancer association rank (Open Targets Platform) across primary sites)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"fixed-4","dir":"Articles","previous_headings":"Version 1.0.6","what":"Fixed","title":"Changelog","text":"Report disclaimer occurring bottom report longer missing web-based analysis (oncotools.elixir.) - file _site.yml inst/templates","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"resources---overview","dir":"Articles","previous_headings":"","what":"Resources - overview","title":"Annotation resources","text":"Data harvested integrated following resources form backbone oncoEnrichR: Open Targets Platform - human drug-target associations comprehensive disease-target associations CancerMine - literature-mined database drivers, oncogenes tumor suppressors cancer Network Cancer Genes - Network cancer genes - web resource analyze duplicability, orthology network properties cancer genes IntOGen - Compendium mutational driver genes cancer UniProt Cancer Gene Census DoRothEA - gene set resource containing signed transcription factor (TF) - target (regulatory) interactions CellChatDB - ligand-receptor interaction resource Cancer Genome Atlas (TCGA) - gene aberration frequencies, recurrent point mutations/indels, co-expression patterns ~9,500 primary tumor samples Human Protein Atlas - expression data healthy human tissues (GTex)/cell types, prognostic gene expression associations cancer Molecular Signatures Database (MSigDB) - collection annotated (e.g. towards pathways) genesets enrichment/-representation analysis. includes genesets Gene Ontology, Reactome, KEGG, WikiPathways, BIOCARTA, well curated immunologic cancer-specific signatures. NetPath - signaling transduction pathways Pfam - protein domain database STRING - protein-protein interaction database BioGRID - biomedical interaction repository data compiled comprehensive curation efforts CORUM - protein complex database Compleat - protein complex resource ComplexPortal - manually curated, encyclopaedic resource macro-molecular complexes hu.MAP2 - human protein complex map COMPARTMENTS - subcellular compartment database DepMap/Project Score - Databases effects cancer cell line viability elicited CRISPR-Cas9 mediated gene activation Genetic determinants survival cancer - Resource relative prognostic impact gene mutation, expression, methylation, CNA human cancers Predicted synthetic lethality interactions - Resource predicted synthetic lethality interactions human gene paralogs (using human cancer cell lines)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"resources---annotation-types","dir":"Articles","previous_headings":"","what":"Resources - annotation types","title":"Annotation resources","text":"section describes underlying annotation types oncoEnrichR detail, extent subject quality control/filtering use within package.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"target-disease-associations","dir":"Articles","previous_headings":"Resources - annotation types","what":"Target-disease associations","title":"Annotation resources","text":"Associations genes diseases/tumor types harvested Open Targets Platform. increase confidence target-disease associations shown, include associations support least two data types. weak associations, .e. overall score less 0.05, excluded (complete range 0-1).","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"target-drug-associations","dir":"Articles","previous_headings":"Resources - annotation types","what":"Target-drug associations","title":"Annotation resources","text":"Target-drug associations primarily harvested Open Targets Platform. use phenOncoX R package, dedicated resource phenotype ontology mapping cancer, ensure target-drug associations included oncoEnrichR exclusively cancer conditions.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"tumor-suppressorproto-oncogenecancer-driver-annotation","dir":"Articles","previous_headings":"Resources - annotation types","what":"Tumor suppressor/proto-oncogene/cancer driver annotation","title":"Annotation resources","text":"assign three confidence levels respect genes oncogenic /tumor suppressive roles Strong_support (> 20 citations) biomedical literature (CancerMine), curated entry Network Cancer Genes (NCG) Cancer Gene Census (CGC), Manually curated entry NCG CGC, significant support (> 10 citations) biomedical literature (CancerMine) Curated entry NCG CGC, moderate support (<= 10 citations, > 5 citations) biomedical literature (CancerMine), Significant support (> 10 citations, <= 20 citations) biomedical literature (CancerMine), entry CGC/NCG Curated entry NCG/CGC, weak support (<= 5 citations) biomedical literature (CancerMine), Moderate support (<= 10 citations, > 5 citations) biomedical literature (CancerMine), entry CGC/NCG Literature support tumor suppressive role ignored gene 2.5 times much literature support oncogenic role (vice versa) Classification genes potential cancer drivers require support least two following sources: Network Cancer Genes - canonical cancer drivers IntOGen - predicted cancer driver genes Cancer Gene Census - TIER1/2 - curated cancer genes TCGA’s predicted cancer driver genes CancerMine - literature mining resource, considering entries support > 5 citations)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"gene-cancer-hallmark-associations","dir":"Articles","previous_headings":"Resources - annotation types","what":"Gene cancer hallmark associations","title":"Annotation resources","text":"hallmarks cancer comprise six biological capabilities acquired multistep development human tumors. Genes attributed hallmarks cancer retrieved Open Targets Platform/COSMIC","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"gene-copy-number-aberrations-in-tumors-somatic-amplificationshomozygous-deletions","dir":"Articles","previous_headings":"Resources - annotation types","what":"Gene copy number aberrations in tumors (somatic amplifications/homozygous deletions)","title":"Annotation resources","text":"Somatic copy number amplifications homozygous deletions retrieved Cancer Genome Atlas (TCGA), focusing gene-level calls processed copy number variation analysis pipeline. Copy number events included oncoEnrichR limited high-level amplifications (GISTIC2 CNA value: 2) homozygous deletions (GISTIC2 CNA value: -2)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"recurrent-gene-mutations-in-tumors-somatic-snvsindels","dir":"Articles","previous_headings":"Resources - annotation types","what":"Recurrent gene mutations in tumors (somatic SNVs/InDels)","title":"Annotation resources","text":"Recurrent somatic SNVs/InDels (occurring one tumor sample) retrieved Cancer Genome Atlas (TCGA). SNVs/InDels annotated information mutation hotspots cancer (cancerhotspots.org), protein domains PFAM, predicted status loss--function variants (LOFTEE). protein-altering canonical splice site mutations included.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"gene-co-expression-in-tumors-rna-seq","dir":"Articles","previous_headings":"Resources - annotation types","what":"Gene co-expression in tumors (RNA-seq)","title":"Annotation resources","text":"Co-expression correlation coefficients genes tumors pre-calculated, using RNAseq data available Cancer Genome Atlas (TCGA). calculate separate correlation coefficients tumor type, limit pairs co-expressed genes include either tumor suppressor, oncogene, predicted cancer driver (using classification outlined ). strong correlation coefficients (Spearman’s rank >= 0.7 <= -0.7) included","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"molecular-gene-signatures-pathways","dir":"Articles","previous_headings":"Resources - annotation types","what":"Molecular gene signatures / pathways","title":"Annotation resources","text":"comprehensive set pathway annotations molecular gene signatures form basis functional enrichment module offered oncoEnrichR. include diverse set molecular signatures MSigDB, annotations respect molecular function, biological processes cellular components Gene Ontology (GO), pathway annotations KEGG, WikiPathways, NetPath, Reactome","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"celltissue-specific-gene-expression-patterns","dir":"Articles","previous_headings":"Resources - annotation types","what":"Cell/tissue-specific gene expression patterns","title":"Annotation resources","text":"provide tissue- cell-type specific gene expression annotations Human Protein Atlas. Tissue-specific patterns derived Tissue Atlas, tissue specificity derived deep sequencing RNA (RNA-seq) 54 different normal tissue types. putative protein-coding genes classified respect abundance (tissue enriched, tissue enhanced etc.) different tissues. cell type specificity, utilize data Cell Type Atlas. , classification protein-coding genes based single cell type-specific expression 79 different cell types performed; determining types genes elevated (cell type enriched, cell type enhanced etc.) particular cell type compared cell types.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"gene-fitness-effects","dir":"Articles","previous_headings":"Resources - annotation types","what":"Gene fitness effects","title":"Annotation resources","text":"Gene fitness effects retrieved integration data DepMap & Project Score. include data genes statistically significant effect cell fitness cancer cell lines (fitness score considered quantitative measure reduction cell viability elicited gene inactivation, via CRISPR/Cas9 targeting).","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"subcellular-compartment-annotation","dir":"Articles","previous_headings":"Resources - annotation types","what":"Subcellular compartment annotation","title":"Annotation resources","text":"Confidence score target compartment annotation (range 3 5) type channels support annotations ( Knowledge, Text mining Experimental), well required minimum number channels support given target compartment annotation","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"protein-complexes-and-protein-domains","dir":"Articles","previous_headings":"Resources - annotation types","what":"Protein complexes and protein domains","title":"Annotation resources","text":"Protein complex annotations retrieved multiple resources, including CORUM, Compleat, ComplexPortal, hu.MAP2. Protein domains retrieved Pfam","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"protein-protein-interactions","dir":"Articles","previous_headings":"Resources - annotation types","what":"Protein-protein interactions","title":"Annotation resources","text":"Protein-protein interactions members target set explored using data two different resources: required minimum interaction score, limiting interactions retrieved interaction score greater equal threshold. Interaction scores indicators confidence, .e. likely STRING judges interaction true. type network retrieve, either physical functional addition proteins (maximum 50) part query set, interact confidently proteins query set required minimum number evidence items support interaction (.e. multiple types low high-throughput experiments, e.g. affinity capture-MS, affinity capture-Western). Default: 3, maximum: 10 addition proteins (maximum 50) part query set, interact confidently proteins query set","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"gene-regulatory-interactions","dir":"Articles","previous_headings":"Resources - annotation types","what":"Gene regulatory interactions","title":"Annotation resources","text":"Regulatory interactions (TF-target) retrieved DoRothEA resource. Two collections interactions subject overlap query set oncoEnrichR: global set regulatory interactions, many inferred gene expression patterns normal tissues (GTEx), cancer-focused set, latter inferred gene expression patterns tumors (TCGA).","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"prognostic-gene-associations","dir":"Articles","previous_headings":"Resources - annotation types","what":"Prognostic gene associations","title":"Annotation resources","text":"Prognostic associations (gene expression versus survival) collected Human Pathology Atlas, undertaken correlation analyses mRNA expression levels human genes tumor tissue clinical outcome (survival) ~8,000 cancer patients (underlying data TCGA). Correlation analyses resulted 10,000 prognostic genes. show prognostic genes regard cancer type whether favorable unfavorable terms clinical outcome. Furthermore, show prognostic associations established tcga-survival.com, relates various types gene aberrations (expression methylation levels, CNA/mutation status) tumor samples patient survival.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"ligand-receptor-interactions","dir":"Articles","previous_headings":"Resources - annotation types","what":"Ligand-receptor interactions","title":"Annotation resources","text":"Ligand-receptor interactions collected CellChatDB resource. oncoEnrichR module interactions, interactions ligand receptor found query set shown.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"synthetic-lethality-interactions","dir":"Articles","previous_headings":"Resources - annotation types","what":"Synthetic lethality interactions","title":"Annotation resources","text":"Predicted synthetic lethality interactions human gene paralogs collected De Kegel et al., Cell Systems, 2021. Interactions shown members part query set, interactions single member query set present.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/input.html","id":"input-data","dir":"Articles","previous_headings":"","what":"Input data","title":"Input","text":"main input oncoEnrichR list human genes, typically top ranked hits high-throughput screen. gene list can provided using following identifiers: Primary gene symbols (e.g. KRAS) Entrez gene IDs (e.g. 3845) Uniprot accessions (e.g. P01116) Ensembl gene identifiers (e.g. ENSG00000133703) Ensembl transcript identifiers (e.g. ENST00000311936) Ensembl protein identifiers (e.g. ENSP00000308495) RefSeq transcript identifiers (e.g. NM_004985) RefSeq peptide identifiers (e.g. NP_004976) type identifier used specified using --query_id_type argument. Similarly, background gene set specified (--bgset argument, use enrichment analysis), identifier type set --bgset_id_type argument. user submits gene symbols longer considered primary gene symbols, oncoEnrichR attempts map cases synonyms/aliases primary gene symbols.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/input.html","id":"number-of-input-genes","dir":"Articles","previous_headings":"Input data","what":"Number of input genes","title":"Input","text":"order keep size HTML output report manageable level, currently upper limit n = 1000 genes can used input tool. Please also note tool requires n = 2 input genes bare minimum, although analysis modules included/run genes input. IMPORTANT NOTE: Due large size, HTML report can slow load generating full reports maximum number genes (n = 1000). generally recommend use oncoEnrichR smaller querysets (order 100-600), produce reports can efficiently loaded viewed. want submit query pushes limit (n = 1000), recommend carefully configure report contents/modules, sense producing managable reports.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/installation.html","id":"requirementsdependencies","dir":"Articles","previous_headings":"","what":"Requirements/dependencies","title":"Installation","text":"oncoEnrichR requires R (>=4.1)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/installation.html","id":"installation-of-oncoenrichr-with-r-commands","dir":"Articles","previous_headings":"","what":"Installation of oncoEnrichR with R commands","title":"Installation","text":"install.packages('devtools') devtools::install_github('sigven/oncoEnrichR', ref = \"v1.4.1\") library(oncoEnrichR)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"output-files","dir":"Articles","previous_headings":"","what":"Output files","title":"Output","text":"output analyses performed oncoEnrichR provided two different formats: interactive HTML report multi-sheet Excel workbook","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"html-report","dir":"Articles","previous_headings":"Output files","what":"HTML report","title":"Output","text":", showcase screenshots oncoEnrichR interactive HTML report, following various types questions can answered tool.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"query-verification","dir":"Articles","previous_headings":"Output files > HTML report","what":"Query verification","title":"Output","text":"gene/query identifiers correctly identified? query identifiers outdated, longer considered primary identifier?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"poorly-characterized-genes","dir":"Articles","previous_headings":"Output files > HTML report","what":"Poorly characterized genes","title":"Output","text":"members query set poorly characterized/unknown function?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"cancer-associations","dir":"Articles","previous_headings":"Output files > HTML report","what":"Cancer associations","title":"Output","text":"tumor types associated genes queryset? extents? genes classified tumor suppressors, proto-oncogenes potential cancer driver genes?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"cancer-hallmark-evidence","dir":"Articles","previous_headings":"Output files > HTML report","what":"Cancer hallmark evidence","title":"Output","text":"genes attributed hallmarks cancer?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"drug-associations","dir":"Articles","previous_headings":"Output files > HTML report","what":"Drug associations","title":"Output","text":"available targeted cancer drugs query set members? cancer indications approved drugs targeted towards query set members? target tractabilities query set members?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"synthetic-lethality","dir":"Articles","previous_headings":"Output files > HTML report","what":"Synthetic lethality","title":"Output","text":"genes predicted take part synthetic lethality interactions?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"gene-fitness-scores","dir":"Articles","previous_headings":"Output files > HTML report","what":"Gene fitness scores","title":"Output","text":"members query set significant effect cell fitness, considering large-scale genome-wide CRISPR–Cas9 dropout screening data cancer cell lines?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"protein-complexes","dir":"Articles","previous_headings":"Output files > HTML report","what":"Protein complexes","title":"Output","text":"members query set involved cancer-relevant protein complexes?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"protein-domains","dir":"Articles","previous_headings":"Output files > HTML report","what":"Protein domains","title":"Output","text":"protein domains frequent among members query set?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"protein-protein-interaction-network","dir":"Articles","previous_headings":"Output files > HTML report","what":"Protein-protein interaction network","title":"Output","text":"protein-protein interactions represented query set? proteins hubs interaction network? members query set form community structures network?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"regulatory-interactions","dir":"Articles","previous_headings":"Output files > HTML report","what":"Regulatory interactions","title":"Output","text":"transcriptional regulatory interactions query set? TF/regulator target present? regulatory targets TFs present? regulators targets?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"subcellular-compartments","dir":"Articles","previous_headings":"Output files > HTML report","what":"Subcellular compartments","title":"Output","text":"subcellular compartments represented query set?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"function-and-pathway-enrichment","dir":"Articles","previous_headings":"Output files > HTML report","what":"Function and pathway enrichment","title":"Output","text":"biological pathways/processes, molecular functions, cancer gene signatures enriched query set?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"tissue-and-cell-type-enrichment","dir":"Articles","previous_headings":"Output files > HTML report","what":"Tissue and cell type enrichment","title":"Output","text":"tissue- cell-type specific expression patterns query genes normal/healthy tissue?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"tumor-aberration-frequencies","dir":"Articles","previous_headings":"Output files > HTML report","what":"Tumor aberration frequencies","title":"Output","text":"extent genes query set mutated tumor samples, copy number alterations point mutations/indels?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"tumor-co-expression","dir":"Articles","previous_headings":"Output files > HTML report","what":"Tumor co-expression","title":"Output","text":"members query set co-expressed cancer genes tumor samples?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"prognostic-associations","dir":"Articles","previous_headings":"Output files > HTML report","what":"Prognostic associations","title":"Output","text":"genes linked survival cancer patients, considering expression methylation levels, mutation status query genes tumor samples?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"excel-workbook","dir":"Articles","previous_headings":"Output files","what":"Excel workbook","title":"Output","text":"Excel workbook contains results various analyses conducted, organized multiple sheets (indicated red circles screenshot )","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/running.html","id":"key-functions","dir":"Articles","previous_headings":"","what":"Key functions","title":"Running","text":"oncoEnrichR performs operations following three functions:","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/running.html","id":"oncoenrichrload_db","dir":"Articles","previous_headings":"Key functions","what":"1. oncoEnrichR::load_db()","title":"Running","text":"Loads underlying annotation data repository oncoEnrichR, saves local cache directory. Utilizing googledrive R package","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/running.html","id":"oncoenrichronco_enrich","dir":"Articles","previous_headings":"Key functions","what":"2. oncoEnrichR::onco_enrich()","title":"Running","text":"Consists two main processing steps: 1) Takes input/query list human gene/protein identifiers (e.g. UniProt accession, RefSeq/Ensembl transcript identifer etc.) input conducts uniform identifier conversion 2) Performs extensive annotation, enrichment membership analyses query set underlying data sources cancer-relevant properties human genes interrelationships. Technically, method returns list object contents analyses performed. specific arguments/options default values outlined : See detailed descriptions options ","code":"onco_enrich(   query = NULL,   oeDB = NULL,   query_id_type = \"symbol\",   ignore_id_err = TRUE,   html_floating_toc = T,   html_report_theme = \"default\",   project_title = \"_Project title_\",   project_owner = \"_Project owner_\",   project_description = \"_Project description_\",   bgset = NULL,   bgset_id_type = \"symbol\",   bgset_description = \"All protein-coding genes\",   enrichment_p_value_cutoff = 0.05,   enrichment_p_value_adj = \"BH\",   enrichment_q_value_cutoff = 0.2,   enrichment_min_geneset_size = 10,   enrichment_max_geneset_size = 500,   enrichment_plot_num_terms = 20,   enrichment_simplify_go = TRUE,   subcellcomp_min_confidence = 3,   subcellcomp_min_channels = 1,   subcellcomp_show_cytosol = FALSE,   regulatory_min_confidence = \"D\",   fitness_max_score = -2,   ppi_add_nodes = 30,   ppi_string_min_score = 0.9,   ppi_string_network_type = \"functional\",   ppi_biogrid_min_evidence = 3,   ppi_node_shadow = TRUE,   ppi_show_drugs = TRUE,   ppi_show_isolated_nodes = FALSE,   show_ppi = TRUE,   show_disease = TRUE,   show_top_diseases_only = TRUE,   show_cancer_hallmarks = TRUE,   show_drug = TRUE,   show_enrichment = TRUE,   show_aberration = TRUE,   show_coexpression = TRUE,   show_cell_tissue = FALSE,   show_ligand_receptor = TRUE,   show_regulatory = TRUE,   show_unknown_function = TRUE,   show_prognostic = TRUE,   show_subcell_comp = TRUE,   show_synleth = TRUE,   show_fitness = TRUE,   show_complex = TRUE,   show_domain = TRUE)"},{"path":"https://sigven.github.io/oncoEnrichR/articles/running.html","id":"oncoenrichrwrite","dir":"Articles","previous_headings":"Key functions","what":"3. oncoEnrichR::write()","title":"Running","text":"Consists two main processing steps: 1) Transformation raw analysis results returned oncoEnrichR::onco_enrich() various visualizations interactive tables 2) Assembly generation final analysis report ) structured interactive oncoEnrichR HTML report B) multisheet Excel workbook","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/running.html","id":"example-run","dir":"Articles","previous_headings":"","what":"Example run","title":"Running","text":"target list n = 134 high-confidence interacting proteins c-MYC oncoprotein previously identified BioID protein proximity assay standard cell culture tumor xenografts (Dingar et al., J Proteomics, 2015). ran target list oncoEnrichR analysis workflow using following configurations onco_enrich method: project_title = \"cMYC_BioID_screen\" project_owner = \"Raught et al.\" produced following HTML report results. R commands provided reproduce example output. NOTE: Replace “LOCAL_FOLDER” directory local computer: library(oncoEnrichR) myc_interact_targets <- read.csv(system.file(\"extdata\",\"myc_data.csv\", package = \"oncoEnrichR\"), stringsAsFactors = F) oeDB <- oncoEnrichR::load_db(cache_dir = \"LOCAL_FOLDER\") myc_report <- oncoEnrichR::onco_enrich(query = myc_interact_targets$symbol, oeDB = oeDB, show_cell_tissue = T, project_title = \"cMYC_BioID_screen\", project_owner = \"Raught et al.\") oncoEnrichR::write(report = myc_report, oeDB = oeDB, file = \"LOCAL_FOLDER/myc_report_oncoenrichr.html\", format = \"html\") oncoEnrichR::write(report = myc_report, oeDB = oeDB, file = \"LOCAL_FOLDER/myc_report_oncoenrichr.xlsx\", format = \"excel\")","code":""},{"path":"https://sigven.github.io/oncoEnrichR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sigve Nakken. Author, maintainer.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sigve Nakken, Sveinung Gundersen, Fabian L. M. Bernal, Eivind Hovig, Jørgen Wesche. OncoEnrichR: cancer-dedicated gene set interpretation (2021). arXiv:2107.13247v2. https://arxiv.org/abs/2107.13247v2","code":"@Misc{,   title = {oncoEnrichR: cancer-dedicated gene set interpretation},   author = {Sigve Nakken and Sveinung Gundersen and Fabian L. M. Bernal and Eivind Hovig and Jørgen Wesche},   year = {2021},   eprint = {2107.13247v2},   archiveprefix = {arXiv},   primaryclass = {q-bio.GN},   url = {https://arxiv.org/abs/2107.13247v2}, }"},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"oncoenrichr-","dir":"","previous_headings":"","what":"Cancer-dedicated gene set interpretation","title":"Cancer-dedicated gene set interpretation","text":"oncoEnrichR R package functional interrogation human genesets context cancer. primarily intended exploratory analysis, interpretation, prioritization long gene lists, represent common output many types high-throughput cancer biology screens. oncoEnrichR can used interrogate results e.g. genetic screens (siRNA/CRISPR), protein proximity labeling, transcriptomics (differential expression). tool queries variety high-quality data resources order assemble useful gene annotations analyses interactive report (examples report shown ). Web-based access oncoEnrichR available  https://oncotools.elixir.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"questions-addressed-by-oncoenrichr","dir":"","previous_headings":"","what":"Questions addressed by oncoEnrichR","title":"Cancer-dedicated gene set interpretation","text":"contents analysis report provided oncoEnrichR address following scientific questions given gene list: diseases/tumor types known associated genes query set, extent? genes query set known oncogenic tumor suppressive roles, using evidence biomedical literature curated resources? genes query set attributed cancer hallmark evidence? proteins query sets druggable different cancer conditions (early late clinical development phases)? proteins query set, likelihood druggable? protein complexes involve proteins query set? subcellular compartments (nucleus, cytosol, plasma membrane etc) dominant localizations proteins query set? specific tissues cell types enriched query set, considering tissue/cell-type specific expression patterns target genes? protein-protein interactions known within query set? interactions members query set cancer-relevant proteins (e.g. proto-oncogenes, tumor-suppressors predicted cancer drivers)? proteins constitute hubs protein-protein interaction network? known regulatory interactions (TF-target) found within query set, mode regulation (repressive vs. stimulating)? occurrences known ligand-receptor interactions within query set? specific pathways, biological processes, pre-defined molecular signatures enriched within query set, compared reference/background set? members query set frequently mutated tumor sample cohorts (TCGA, SNVs/InDels, homozygous deletions, copy number amplifications)? members query set co-expressed (strong negative positive correlations) cancer-relevant genes (.e. proto-oncogenes tumor suppressors) tumor sample cohorts (TCGA)? members query set associated better/worse survival different cancers, considering high low gene expression levels, mutation, copy number status tumors? members query set predicted partners synthetic lethality interactions? members query set associated cellular loss--fitness CRISPR/Cas9 whole-genome drop screens cancer cell lines (.e. reduction cell viability elicited gene inactivation)? targets prioritized therapeutic targets, considering fitness effects genomic biomarkers combination? See also output views addresses questions .","code":""},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"news","dir":"","previous_headings":"","what":"News","title":"Cancer-dedicated gene set interpretation","text":"June 18th 2023: 1.4.1 release February 21st 2023: 1.4.0 release September 27th 2022: 1.3.2 release","code":""},{"path":[]},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Cancer-dedicated gene set interpretation","text":"Installation instructions run oncoEnrichR Explore various analysis outputs produced oncoEnrichR Annotation resources available oncoEnrichR","code":""},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"contact","dir":"","previous_headings":"","what":"Contact","title":"Cancer-dedicated gene set interpretation","text":"sigven ifi.uio.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"funding-and-collaboration","dir":"","previous_headings":"","what":"Funding and Collaboration","title":"Cancer-dedicated gene set interpretation","text":"oncoEnrichR supported Centre Cancer Cell Reprogramming University Oslo/Oslo University Hospital, Elixir Norway (Oslo node).        ","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/gseabase.html","id":null,"dir":"Reference","previous_headings":"","what":"GSEAbase imports — gseabase","title":"GSEAbase imports — gseabase","text":"GSEAbase imports","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/init_report.html","id":null,"dir":"Reference","previous_headings":"","what":"Load oncoEnrichR annotation database — init_report","title":"Load oncoEnrichR annotation database — init_report","text":"Load oncoEnrichR annotation database","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/init_report.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load oncoEnrichR annotation database — init_report","text":"","code":"init_report(   oeDB,   project_title = \"_Project title_\",   project_owner = \"_Project owner_\",   html_floating_toc = T,   html_report_theme = \"default\",   query_id_type = \"symbol\",   ignore_id_err = TRUE,   project_description = \"_Project description_\",   ppi_string_min_score = 0.9,   ppi_string_network_type = \"functional\",   ppi_biogrid_min_evidence = 3,   ppi_add_nodes = 30,   ppi_show_isolated_nodes = FALSE,   ppi_node_shadow = TRUE,   ppi_show_drugs = T,   bgset_description = \"All annotated protein-coding genes\",   bgset_id_type = \"symbol\",   enrichment_p_value_cutoff = 0.05,   enrichment_p_value_adj = \"BH\",   enrichment_q_value_cutoff = 0.2,   enrichment_min_geneset_size = 10,   enrichment_max_geneset_size = 500,   enrichment_plot_num_terms = 20,   enrichment_simplify_go = F,   subcellcomp_min_confidence = 3,   subcellcomp_min_channels = 1,   subcellcomp_show_cytosol = F,   regulatory_min_confidence = \"D\",   fitness_max_score = -2,   show_ppi = T,   show_disease = T,   show_top_diseases_only = T,   show_cancer_hallmarks = T,   show_drug = T,   show_enrichment = T,   show_aberration = T,   show_coexpression = T,   show_subcell_comp = T,   show_fitness = T,   show_cell_tissue = F,   show_ligand_receptor = T,   show_regulatory = T,   show_unknown_function = T,   show_prognostic = T,   show_synleth = T,   show_complex = T,   show_domain = T )"},{"path":"https://sigven.github.io/oncoEnrichR/reference/init_report.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load oncoEnrichR annotation database — init_report","text":"oeDB oncoEnrichR annotation database object project_title project title (title report) project_owner name project owner html_floating_toc logical - float table contents left main document content. floating table contents always visible even document scrolled html_report_theme Bootswatch theme HTML report (\"bootstrap\",\"cerulean\",\"cosmo\",\"default\",\"flatly\",\"journal\",\"lumen\",\"paper\",\"sandstone\",\"simplex\",\"spacelab\",\"united\",\"yeti\") query_id_type character indicating source query (one \"uniprot_acc\", \"symbol\", \"entrezgene\", \"ensembl_gene\",\"ensembl_mrna\",\"refseq_mrna\",\"ensembl_protein\",\"refseq_protein\") ignore_id_err logical indicating analysis continue uknown query identifiers encountered project_description project background information ppi_string_min_score minimum score (0 1) confidence retrieved protein-protein interactions (STRING) ppi_string_network_type STRING network type ('physical' 'functional') ppi_biogrid_min_evidence minimum number evidence items protein-protein interactions shown (BIOGRID) ppi_add_nodes number nodes add target set computing protein-protein interaction network (STRING/BIOGRID) ppi_show_isolated_nodes logical indicating targets/nodes without interactions displayed protein-protein interaction network ppi_node_shadow show shadow nodes displayed PPI network (STRING/BIOGRID) ppi_show_drugs logical indicating targeted drugs (> phase 3) displayed protein-protein interaction network bgset_description character indicating type background (e.g. \"lipid-binding proteins (n = 200)\") bgset_id_type character indicating source query (one \"uniprot_acc\", \"symbol\", \"entrezgene\", \"ensembl_gene\",\"ensembl_mrna\",\"refseq_mrna\",\"ensembl_protein\",\"refseq_protein\") enrichment_p_value_cutoff cutoff p-value enrichment/-representation analysis enrichment_p_value_adj one \"holm\", \"hochberg\", \"hommel\", \"bonferroni\", \"BH\", \"\", \"fdr\", \"none\" enrichment_q_value_cutoff cutoff q-value enrichment analysis enrichment_min_geneset_size minimal size geneset annotated term testing enrichment/-representation analysis enrichment_max_geneset_size maximal size geneset annotated term testing enrichment/-representation analysis enrichment_plot_num_terms number top enriched Gene Ontology terms (max) show enrichment barplot enrichment_simplify_go remove highly similar GO terms results GO enrichment/-representation analysis subcellcomp_min_confidence minimun confidence level subcellular compartment annotation COMPARTMENTS (min = 3, max = 5) subcellcomp_min_channels minimum number channels support subcellular annotation COMPARTMENTS subcellcomp_show_cytosol logical indicating subcellular heatmap highlight cytosol subcellular protein location regulatory_min_confidence minimum confidence level regulatory interactions (TF-target) retrieved DoRothEA ('','B','C', 'D') fitness_max_score maximum loss--fitness score (scaled Bayes factor BAGEL) genes retrieved Project Score show_ppi logical indicating report contain protein-protein interaction data (STRING) show_disease logical indicating report contain disease associations (Open Targets Platform, association_score >= 0.05, support least two data types) show_top_diseases_only logical indicating report contain top (n = 20) disease associations pr. query gene (Open Targets Platform) show_cancer_hallmarks logical indicating report contain annotations/evidence cancer hallmarks per query gene (COSMIC/Open Targets Platform) show_drug logical indicating report contain targeted cancer drug information show_enrichment logical indicating report contain functional enrichment/-representation analysis (MSigDB, GO, KEGG, REACTOME, NetPath, WikiPathways) show_aberration logical indicating report contain TCGA aberration plots (amplifications/deletions) show_coexpression logical indicating report contain TCGA co-expression data (RNAseq) query set oncogenes/tumor suppressor genes show_subcell_comp logical indicating report provide subcellular compartment annotations (COMPARTMENTS) show_fitness logical indicating report provide fitness scores target priority scores CRISPR/Cas9 loss--fitness screens (Project Score) show_cell_tissue logical indicating report contain tissue-specificity single cell-type specificity assessments (Human Protein Atlas) target genes, using data Human Protein Atlas show_ligand_receptor logical indicating report contain ligand-receptor interactions (CellChatDB) show_regulatory logical indicating report contain data transcription factor (TF) - target interactions relevant query set (DoRothEA) show_unknown_function logical indicating report highlight target genes unknown poorly defined functions (GO/Uniprot KB/NCBI) show_prognostic logical indicating mRNA-based (single-gene) prognostic associations cancer types listed (Human Protein Atlas/TCGA) show_synleth logical indicating report list overlap predicted synthetic lethality interactions (gene paralogs , De Kegel et al., Cell Systems, 2021) show_complex logical indicating report provide target memberships known protein complexes (ComplexPortal/Compleat/PDB/CORUM) show_domain logical indicating report provide target memberships known protein domains (Pfam) remote TRUE (default), load database version-tagged Zenodo repository cache_dir path local cache efficient subsequent loads","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/load_db.html","id":null,"dir":"Reference","previous_headings":"","what":"Load oncoEnrichR data repository — load_db","title":"Load oncoEnrichR data repository — load_db","text":"Function fetches version-tagged oncoEnrichR data repository Google Drive","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/load_db.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load oncoEnrichR data repository — load_db","text":"","code":"load_db(cache_dir = NA, force_download = FALSE, googledrive = TRUE)"},{"path":"https://sigven.github.io/oncoEnrichR/reference/load_db.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load oncoEnrichR data repository — load_db","text":"cache_dir Local directory data download force_download Logical indicating local cache force download (.e. set TRUE re-download even data exists cache) googledrive logical indicating use googledrive UiO server host downloading","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/load_db.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load oncoEnrichR data repository — load_db","text":"list object oncoEnrichR datasets, used oeDB argument onco_enrich() write()","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/onco_enrich.html","id":null,"dir":"Reference","previous_headings":"","what":"Interrogate a gene list for cancer relevance — onco_enrich","title":"Interrogate a gene list for cancer relevance — onco_enrich","text":"Function interrogates list human gene identifiers cancer relevance. Multiple perspectives offered, including tumor aberration co-expression patterns, druggability, protein-protein interactions, gene fitness effects, regulatory interactions, subcellular compartment enrichment, pathway enrichment, synthetic lethality interactions, prognostic associations, .","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/onco_enrich.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Interrogate a gene list for cancer relevance — onco_enrich","text":"","code":"onco_enrich(   query = NULL,   oeDB = NULL,   query_id_type = \"symbol\",   ignore_id_err = TRUE,   html_floating_toc = T,   html_report_theme = \"default\",   project_title = \"_Project title_\",   project_owner = \"_Project owner_\",   project_description = \"_Project description_\",   bgset = NULL,   bgset_id_type = \"symbol\",   bgset_description = \"All protein-coding genes\",   enrichment_p_value_cutoff = 0.05,   enrichment_p_value_adj = \"BH\",   enrichment_q_value_cutoff = 0.2,   enrichment_min_geneset_size = 10,   enrichment_max_geneset_size = 500,   enrichment_plot_num_terms = 20,   enrichment_simplify_go = TRUE,   subcellcomp_min_confidence = 3,   subcellcomp_min_channels = 1,   subcellcomp_show_cytosol = FALSE,   regulatory_min_confidence = \"D\",   fitness_max_score = -2,   ppi_add_nodes = 30,   ppi_string_min_score = 0.9,   ppi_string_network_type = \"functional\",   ppi_biogrid_min_evidence = 3,   ppi_node_shadow = TRUE,   ppi_show_drugs = TRUE,   ppi_show_isolated_nodes = FALSE,   show_ppi = TRUE,   show_disease = TRUE,   show_top_diseases_only = TRUE,   show_cancer_hallmarks = TRUE,   show_drug = TRUE,   show_enrichment = TRUE,   show_aberration = TRUE,   show_coexpression = TRUE,   show_cell_tissue = FALSE,   show_ligand_receptor = TRUE,   show_regulatory = TRUE,   show_unknown_function = TRUE,   show_prognostic = TRUE,   show_subcell_comp = TRUE,   show_synleth = TRUE,   show_fitness = TRUE,   show_complex = TRUE,   show_domain = TRUE,   ... )"},{"path":"https://sigven.github.io/oncoEnrichR/reference/onco_enrich.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Interrogate a gene list for cancer relevance — onco_enrich","text":"query character vector gene/query identifiers (minimum 2, maximum 1000) oeDB oncoEnrichR data repository object - returned load_db() query_id_type character indicating source query (one \"uniprot_acc\", \"symbol\",\"entrezgene\", \"ensembl_gene\", \"ensembl_mrna\", \"refseq_mrna\", \"ensembl_protein\", \"refseq_protein\") ignore_id_err logical indicating analysis continue uknown query identifiers encountered html_floating_toc logical - float table contents left main document content (HTML report). floating table contents always visible even document scrolled html_report_theme Bootswatch theme HTML report (\"bootstrap\", \"cerulean\", \"cosmo\", \"default\", \"flatly\", \"journal\", \"lumen\", \"paper\", \"sandstone\", \"simplex\", \"spacelab\", \"united\", \"yeti\") project_title project title (title report) project_owner name project owner project_description project background information bgset character vector gene identifiers, used reference/background enrichment/-representation analysis bgset_id_type character indicating source background (\"uniprot_acc\", \"symbol\", \"entrezgene\", \"ensembl_gene\", \"ensembl_mrna\", \"refseq_mrna\", \"ensembl_protein\", \"refseq_protein\"), default: \"symbol\" bgset_description character indicating type background (e.g. \"lipid-binding proteins (n = 200)\") enrichment_p_value_cutoff cutoff p-value enrichment/ -representation analysis (default: 0.05) enrichment_p_value_adj one \"holm\", \"hochberg\", \"hommel\", \"bonferroni\", \"BH\", \"\", \"fdr\", \"none\" (clusterProfiler, default: \"BH\") enrichment_q_value_cutoff cutoff q-value enrichment analysis (clusterProfiler, default: 0.2) enrichment_min_geneset_size minimal size geneset annotated term testing enrichment/-representation analysis (clusterProfiler, default: 10) enrichment_max_geneset_size maximal size geneset annotated term testing enrichment/-representation analysis (clusterProfiler, default: 500) enrichment_plot_num_terms number top enriched Gene Ontology terms (max) show enrichment barplot (default: 15) enrichment_simplify_go remove highly similar GO terms results GO enrichment/-representation analysis (default: TRUE) subcellcomp_min_confidence minimum confidence level subcellular compartment annotation COMPARTMENTS (min = 3, max = 5, default: 3) subcellcomp_min_channels minimum number channels support subcellular compartment annotation COMPARTMENTS (min = 1, max = 3, default: 1) subcellcomp_show_cytosol logical indicating subcellular heatmap show highlight proteins located cytosol (default: FALSE) regulatory_min_confidence minimum confidence level regulatory interactions (TF-target) retrieved DoRothEA ('','B','C', 'D', default: 'D') fitness_max_score maximum loss--fitness score (scaled Bayes factor BAGEL) genes retrieved DepMap/Project Score, default:-2 ppi_add_nodes number nodes add target set computing protein-protein interaction network (STRING/BioGRID, default: 30) ppi_string_min_score minimum score (0 1) confidence retrieved protein-protein interactions (STRING, default: 0.9) ppi_string_network_type type network show interactions STRING ('functional' 'physical', default: 'functional') ppi_biogrid_min_evidence minimum number evidence items required protein-protein interactions retrieved (BioGRID, default: 3) ppi_node_shadow show shadow nodes displayed PPI network (default: TRUE) ppi_show_drugs logical indicating targeted drugs (>= phase 3) displayed protein-protein interaction networks (default: TRUE) ppi_show_isolated_nodes logical indicating targets/nodes without interactions displayed protein-protein interaction networks (default: FALSE) show_ppi logical indicating report contain protein-protein interaction views query set (STRING BioGRID, default: TRUE) show_disease logical indicating report contain disease associations (Open Targets Platform, association_score >= 0.05, support least two data types), tumor suppressor/oncogene annotations ( default: TRUE) show_top_diseases_only logical indicating report contain top (n = 20) disease associations pr. query gene default: TRUE) show_cancer_hallmarks logical indicating report contain annotations/evidence cancer hallmarks per query gene (COSMIC/Open Targets Platform, default: TRUE show_drug logical indicating report contain targeted cancer drug information (default: TRUE) show_enrichment logical indicating report contain functional enrichment/-representation analysis (MSigDB, GO, KEGG, REACTOME, NetPath, WikiPathways, default: TRUE) show_aberration logical indicating report contain TCGA aberration plots (amplifications/deletions, default: TRUE) show_coexpression logical indicating report contain TCGA co-expression data (RNAseq) query set oncogenes/tumor suppressor genes (default: TRUE) show_cell_tissue logical indicating report contain tissue-specificity single cell-type specificity assessments (Human Protein Atlas) target genes (default: FALSE) show_ligand_receptor logical indicating report contain ligand-receptor interactions (CellChatDB, default: TRUE) show_regulatory logical indicating report contain data transcription factor (TF) - target interactions relevant query set (DoRothEA, default: TRUE) show_unknown_function logical indicating report highlight target genes unknown poorly defined functions (GO/Uniprot KB/NCBI, default: TRUE) show_prognostic logical indicating mRNA-based (single-gene) prognostic associations cancer types listed (Human Protein Atlas/TCGA, default: TRUE show_subcell_comp logical indicating report provide subcellular compartment annotations (COMPARTMENTS, default: TRUE) show_synleth logical indicating report list overlap predicted synthetic lethality interactions (gene paralogs , De Kegel et al., Cell Systems, 2021). Default: TRUE show_fitness logical indicating report provide fitness scores target priority scores CRISPR/Cas9 loss--fitness screens (DepMap/Project Score, default: TRUE) show_complex logical indicating report provide target memberships known protein complexes (ComplexPortal/Compleat/hu.MAP2/PDB/CORUM, default: TRUE) show_domain logical indicating report provide target memberships known protein domains (Pfam, default: TRUE) ... arguments Galaxy/web-based processing","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/onco_enrich.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Interrogate a gene list for cancer relevance — onco_enrich","text":"oncoEnrichR report list object, two main elements, data config. data contains data goes section output reports, config contains metadata annotation resources used.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/tidyeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy eval helpers — tidyeval","title":"Tidy eval helpers — tidyeval","text":"https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/url_exists.html","id":null,"dir":"Reference","previous_headings":"","what":"RCurl url.exists — url_exists","title":"RCurl url.exists — url_exists","text":"RCurl url.exists","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that validates the oncoEnrichR database object — validate_db","title":"Function that validates the oncoEnrichR database object — validate_db","text":"Function validates oncoEnrichR database object","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that validates the oncoEnrichR database object — validate_db","text":"","code":"validate_db(oe_db)"},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that validates the oncoEnrichR database object — validate_db","text":"db list object annotation data oncoEnrichR","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that validates a particular db object (data.frame) in oncoEnrichR — validate_db_df","title":"Function that validates a particular db object (data.frame) in oncoEnrichR — validate_db_df","text":"Function validates particular db object (data.frame) oncoEnrichR","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that validates a particular db object (data.frame) in oncoEnrichR — validate_db_df","text":"","code":"validate_db_df(df, dbtype = \"genedb\")"},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that validates a particular db object (data.frame) in oncoEnrichR — validate_db_df","text":"df data.frame annotation data oncoEnrichR dbtype type oncoEnrichR datasource","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/write.html","id":null,"dir":"Reference","previous_headings":"","what":"Write oncoEnrichR report object to output file — write","title":"Write oncoEnrichR report object to output file — write","text":"Function writes oncoEnrichR report object file, either interactive HTML report Excel workbook.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/write.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write oncoEnrichR report object to output file — write","text":"","code":"write(   report,   oeDB,   file = \"testReport.html\",   ignore_file_extension = F,   overwrite = F,   format = \"html\",   ... )"},{"path":"https://sigven.github.io/oncoEnrichR/reference/write.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write oncoEnrichR report object to output file — write","text":"report object oncoEnrichR report data (returned oeDB$onco_enrich) oeDB oncoEnrichR data repository object - returned load_db() file full filename report output (e.g. \"oe_report.html\" \"oe_report.xlsx\") ignore_file_extension logical accept type filaname extensions (Galaxy integration) overwrite logical indicating existing output files may overwritten format file format output (html/excel) ... options Galaxy/non self-contained HTML. applicable use Galaxy","code":""}]
+[{"path":"https://sigven.github.io/oncoEnrichR/CODE_OF_CONDUCT.html","id":null,"dir":"","previous_headings":"","what":"Contributor Code of Conduct","title":"Contributor Code of Conduct","text":"contributors maintainers project, pledge respect people contribute reporting issues, posting feature requests, updating documentation, submitting pull requests patches, activities. committed making participation project harassment-free experience everyone, regardless level experience, gender, gender identity expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, religion. Examples unacceptable behavior participants include use sexual language imagery, derogatory comments personal attacks, trolling, public private harassment, insults, unprofessional conduct. Project maintainers right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct. Project maintainers follow Code Conduct may removed project team. Instances abusive, harassing, otherwise unacceptable behavior may reported opening issue contacting one project maintainers. Code Conduct adapted Contributor Covenant (http://contributor-covenant.org), version 1.0.0, available http://contributor-covenant.org/version/1/0/0/","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-4-2","dir":"Articles","previous_headings":"","what":"Version 1.4.2","title":"Changelog","text":"Date: 2023-08-16","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed","dir":"Articles","previous_headings":"Version 1.4.2","what":"Changed","title":"Changelog","text":"WikiPathways (20230810) COMPARTMENTS (2023-08) KEGG (20230710) BioGRID (v4.4.224) Open Targets Platform (2023.06) Experimental Factor Ontology (v3.56.0) Human Disease Ontology (2023-07-20) limited set TCGA amplifications/deletions erroneously left v1.4.1 (gene alias matching) - fixed v1.4.2 Updated Citation Note sections report Fixed typos report template","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-4-1","dir":"Articles","previous_headings":"","what":"Version 1.4.1","title":"Changelog","text":"Date: 2023-06-18","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-1","dir":"Articles","previous_headings":"Version 1.4.1","what":"Changed","title":"Changelog","text":"TCGA (20220329 - v37.0) WikiPathways (20230610) CancerMine (v50, 20230301) COMPARTMENTS (2023-05) KEGG (20230330) BioGRID (v4.4.222) Open Targets Platform (2023.02) Cancer Gene Census (v98) Network Cancer Genes (v7.1) MSigDB (v2023.1.Hs) Experimental Factor Ontology (v3.54.0) Human Disease Ontology (2023-05-31) Added Citation Note section output module - key citations Added data licensing terms Documentation & Settings module","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-4-0","dir":"Articles","previous_headings":"","what":"Version 1.4.0","title":"Changelog","text":"Date: 2023-02-21","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-2","dir":"Articles","previous_headings":"Version 1.4.0","what":"Changed","title":"Changelog","text":"TCGA (20221212 - v36.0) WikiPathways (20230210) CancerMine (20230114) COMPARTMENTS (2023-01) KEGG (20230101) Experimental Factor Ontology (v3.50.0) Human Disease Ontology (2023-01-31) Downloading Google Drive can somethis cause trouble due downloading limitations issued Google. alternative approach, one can now download datasets using another host (server hosted University Oslo), argument googledrive = FALSE oncoEnrichR::load_db() Users can opt show isolated nodes (nodes interactions) - logical argument onco_enrich(): ppi_show_isolated_nodes (default FALSE) Users can set minimum required threshold number evidence items required interaction BioGRID New numerical argument onco_enrich(): ppi_biogrid_min_evidence New character argument onco_enrich(): ppi_string_network_type (physical functional) Previous argument ppi_score_threshold now named ppi_string_min_score, scale goes 0 1 (opposed 0-1000 previous versions) Now using regularly updated COMPARTMENTS resource underlying source annotation New arguments onco_enrich(): subcellcomp_min_confidence, subcellcomp_min_channels revised approach assign roles proto-oncogenes tumor suppressors implemented, assign role confidence level (Moderate/Strong/strong) pending upon support manually curated resources (Network Cancer Genes (NCG) Cancer Gene Census (CGC)) support biomedical literature (CancerMine) conservative approach driver gene status implemented: requiring support least two distinct resources (Network Cancer Genes (NCG), Cancer Gene Census, TCGA, IntOGen, CancerMine) ppi_string_min_score ppi_string_network_type ppi_biogrid_min_evidence ppi_show_drugs ppi_show_isolated_nodes regulatory_min_confidence enrichment_p_value_cutoff enrichment_q_value_cutoff enrichment_p_value_adj enrichment_plot_num_terms enrichment_simplify_go enrichment_max_geneset_size enrichment_min_geneset_size subcellcomp_min_confidence subcellcomp_show_cytosol subcellcomp_min_channels added oncoEnrichR favicon output HTML reports","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-3-2","dir":"Articles","previous_headings":"","what":"Version 1.3.2","title":"Changelog","text":"Date: 2022-09-27","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-3","dir":"Articles","previous_headings":"Version 1.3.2","what":"Changed","title":"Changelog","text":"Cancer driver classification Cancer associations section. Driver classification based union IntOGen mutational driver catalogue (v2020-02-01) Network Cancer Genes (canonical drivers, v7.0)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-3-1","dir":"Articles","previous_headings":"","what":"Version 1.3.1","title":"Changelog","text":"Date: 2022-09-23","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added","dir":"Articles","previous_headings":"Version 1.3.1","what":"Added","title":"Changelog","text":"CancerMine (20220920 - v48) TCGA (20220727 - v34.0) WikiPathways (20220910) Experimental Factor Ontology (v3.46.0) Human Disease Ontology (2022-08-29) Recurrent somatic variants (SNVs/InDels, found TCGA) appended Excel output worksheet, tab RECURRENT_VARIANTS","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"fixed","dir":"Articles","previous_headings":"Version 1.3.1","what":"Fixed","title":"Changelog","text":"erroneous mutation hotspots Tumor aberration frequencies section","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-4","dir":"Articles","previous_headings":"Version 1.3.1","what":"Changed","title":"Changelog","text":"Slight modification column names Drug associations section Added links ENSEMBL_GENE_ID Tumor aberration frequencies section","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-3-0","dir":"Articles","previous_headings":"","what":"Version 1.3.0","title":"Changelog","text":"Date: 2022-09-12","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-1","dir":"Articles","previous_headings":"Version 1.3.0","what":"Added","title":"Changelog","text":"MSigDB (August 2022.1)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-5","dir":"Articles","previous_headings":"Version 1.3.0","what":"Changed","title":"Changelog","text":"Fixed artefacts (-AS1 entries) output CancerMine Added approved_drugs column Drug associations section output report","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-2-2","dir":"Articles","previous_headings":"","what":"Version 1.2.2","title":"Changelog","text":"Date: 2022-09-02","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-2","dir":"Articles","previous_headings":"Version 1.2.2","what":"Added","title":"Changelog","text":"WikiPathways (20220810) KEGG (20220809)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-6","dir":"Articles","previous_headings":"Version 1.2.2","what":"Changed","title":"Changelog","text":"Now using googledrive data repository host, due unstable code using Zenodo","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-2-1","dir":"Articles","previous_headings":"","what":"Version 1.2.1","title":"Changelog","text":"Date: 2022-07-13","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-3","dir":"Articles","previous_headings":"Version 1.2.1","what":"Added","title":"Changelog","text":"WikiPathways (20220610) Open Targets Platform (2022.06) CancerMine (v47)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-2-0","dir":"Articles","previous_headings":"","what":"Version 1.2.0","title":"Changelog","text":"Date: 2022-06-24","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-7","dir":"Articles","previous_headings":"Version 1.2.0","what":"Changed","title":"Changelog","text":"Moved zenodo.org hosting underlying datasets, accessed zen4R MAF objects (TCGA) longer loaded GitHub Function oncoEnrichR::write() now requires oncoEnrichR database object (oeDB) argument","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-1-1","dir":"Articles","previous_headings":"","what":"Version 1.1.1","title":"Changelog","text":"Date: 2022-06-16","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-4","dir":"Articles","previous_headings":"Version 1.1.1","what":"Added","title":"Changelog","text":"WikiPathways (20220610) Configurations onco_enrich() populated end HTML report","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-8","dir":"Articles","previous_headings":"Version 1.1.1","what":"Changed","title":"Changelog","text":"show_prognostic_cancer_assoc renamed show_prognostic. show_tcga_aberration renamed show_aberration show_regulatory_interactions renamed show_regulatory show_tcga_coexpression renamed show_coexpression","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"fixed-1","dir":"Articles","previous_headings":"Version 1.1.1","what":"Fixed","title":"Changelog","text":"Bug: database loading missing pfamdb Relaxed dependency versions (caused conflicts R versions < 4.2)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-1-0","dir":"Articles","previous_headings":"","what":"Version 1.1.0","title":"Changelog","text":"Date: 2022-06-10","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-5","dir":"Articles","previous_headings":"Version 1.1.0","what":"Added","title":"Changelog","text":"CancerMine (v46) Open Targets Platform (2022.04) WikiPathways (20220510) GENCODE (v40) CGC (v96) TCGA (GDC release 32) EFO (v42.0) Module shows occurrence protein domains among query set members Protein-complex cancer relevance score ppi_node_shadow - logical indicating nodes PPI network carry shadow show_domain - logical indicating report add section protein domain frequencies query set","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-9","dir":"Articles","previous_headings":"Version 1.1.0","what":"Changed","title":"Changelog","text":"Re-ordering HTML sections, multiple cosmetic changes GO enrichment plots: now showing q-value enrichment factors bar plots Revised method compute tumor-type specific cancer rank (global) Dedicated output article output views sigven.github.io/oncoEnrichR","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"fixed-2","dir":"Articles","previous_headings":"Version 1.1.0","what":"Fixed","title":"Changelog","text":"Bug: duplicate records retrieved co-expression pairs Removed redundant protein complexes OmniPath","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-0-9","dir":"Articles","previous_headings":"","what":"Version 1.0.9","title":"Changelog","text":"Date: 2022-03-31","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-6","dir":"Articles","previous_headings":"Version 1.0.9","what":"Added","title":"Changelog","text":"CancerMine (v43) Open Targets Platform (2022.02) WikiPathways (20220310) Project Score (July 2021 release) add section output option --show_synleth","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"fixed-3","dir":"Articles","previous_headings":"Version 1.0.9","what":"Fixed","title":"Changelog","text":"Bug query identification background set Bug rank top gene-cancer associations","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-10","dir":"Articles","previous_headings":"Version 1.0.9","what":"Changed","title":"Changelog","text":"Option --show_crispr_lof renamed --show_fitness. Corresponding section HTML report renamed CRISPR/Cas9 loss--fitness Gene fitness scores. TCGA co-expression –> Tumor co-expression TCGA aberration frequency —> Tumor aberration frequencies TCGA prognostic associations —> Prognostic associations Sections include tabsets now organized initial active tab always contains data (exception tabs empty)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-0-8","dir":"Articles","previous_headings":"","what":"Version 1.0.8","title":"Changelog","text":"Date: 2022-02-18","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-7","dir":"Articles","previous_headings":"Version 1.0.8","what":"Added","title":"Changelog","text":"WikiPathways (20220210) CancerMine (v42) MSigDB (v7.5.1) GENCODE (v39) Gene summary (NCBI) Reactome/GO (MSigDB v7.5.1) KEGG (20211223)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-11","dir":"Articles","previous_headings":"Version 1.0.8","what":"Changed","title":"Changelog","text":"Refactoring code data mapping gene identifiers Refactoring code database loading","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-0-7","dir":"Articles","previous_headings":"","what":"Version 1.0.7","title":"Changelog","text":"Date: 2021-11-30","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-8","dir":"Articles","previous_headings":"Version 1.0.7","what":"Added","title":"Changelog","text":"WikiPathways (20211110) Open Targets Platform (2021.11) EFO (v3.36.0) TCGA (v31, 2021-10-29) CancerMine (v40) Human Protein Atlas (v21) UniProt KB (2021_04) PFAM domains (release 35, November 2021)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"changed-12","dir":"Articles","previous_headings":"Version 1.0.7","what":"Changed","title":"Changelog","text":"Management annotation databases re-designed, reducing size installation oncoEnrichR significantly. re-design results addition initial step analysis; database loading.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"version-1-0-6","dir":"Articles","previous_headings":"","what":"Version 1.0.6","title":"Changelog","text":"Date: 2021-10-27","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"added-9","dir":"Articles","previous_headings":"Version 1.0.6","what":"Added","title":"Changelog","text":"KEGG (20211013) WikiPathways (20211010) Open Targets Platform (2021.09) EFO (v3.35.0), DiseaseOntology (v2021-10-11) TCGA (v30, 2021-09-23) Protein complex annotations - additions Compleat, ComplexPortal, PDB, hu.MAP2 View overlap members queryset previously established regulatory interactions (TF-target relationships) DoRothEA resource Explore potential ligand-receptor interactions query set, found CellChat database Choose Bootswatch theme HTML report - option html_report_theme Choose table contents placed HTML report (floating-left static top) - option html_floating_toc html_floating_toc - logical, set FALSE, table contents HTML report placed top main document html_report_theme - character, choose different Bootswatch themes style HTML report show_regulatory - logical, show regulatory interactions module (DoRothEA) min_confidence_reg_interaction - character, minimum confidence regulatory interactions included DoRothEA (‘’,‘B’,‘C’, ‘D’) show_ligand_receptor - logical, show ligand-receptor interaction module (CellChatDB) num_terms_enrichment_plot - integer, number enriched Gene Ontology terms (max) show enrichment barplots (module Functional Enrichment) modules Regulatory Interactions Tissue cell type enrichment, interactions/targets ranked according quantitative cancer association score cancer_max_rank (maximum gene-cancer association rank (Open Targets Platform) across primary sites)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html","id":"fixed-4","dir":"Articles","previous_headings":"Version 1.0.6","what":"Fixed","title":"Changelog","text":"Report disclaimer occurring bottom report longer missing web-based analysis (oncotools.elixir.) - file _site.yml inst/templates","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"resources---overview","dir":"Articles","previous_headings":"","what":"Resources - overview","title":"Annotation resources","text":"Data harvested integrated following resources form backbone oncoEnrichR: Open Targets Platform - human drug-target associations comprehensive disease-target associations CancerMine - literature-mined database drivers, proto-oncogenes tumor suppressors cancer Network Cancer Genes - Network cancer genes - web resource analyze duplicability, orthology network properties cancer genes IntOGen - Compendium mutational driver genes cancer UniProt - Comprehensive freely accessible resource protein sequence functional information Cancer Gene Census DoRothEA - gene set resource containing signed transcription factor (TF) - target (regulatory) interactions CellChatDB - ligand-receptor interaction resource Cancer Genome Atlas (TCGA) - gene aberration frequencies, recurrent point mutations/indels, co-expression patterns ~9,500 primary tumor samples Human Protein Atlas - expression data healthy human tissues (GTex)/cell types, prognostic gene expression associations cancer Molecular Signatures Database (MSigDB) - collection annotated (e.g. towards pathways) genesets enrichment/-representation analysis. includes genesets Gene Ontology, Reactome, KEGG, WikiPathways, BIOCARTA, well curated immunologic cancer-specific signatures. NetPath - signaling transduction pathways Pfam - protein domain database STRING - protein-protein interaction database BioGRID - biomedical interaction repository data compiled comprehensive curation efforts CORUM - protein complex database Compleat - protein complex resource ComplexPortal - manually curated, encyclopaedic resource macro-molecular complexes hu.MAP2 - human protein complex map COMPARTMENTS - subcellular compartment database DepMap/Project Score - Databases effects cancer cell line viability elicited CRISPR-Cas9 mediated gene activation Genetic determinants survival cancer - Resource relative prognostic impact gene mutation, expression, methylation, CNA human cancers Predicted synthetic lethality interactions - Resource predicted synthetic lethality interactions human gene paralogs (using human cancer cell lines)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"resources---annotation-types","dir":"Articles","previous_headings":"","what":"Resources - annotation types","title":"Annotation resources","text":"section describes underlying annotation types oncoEnrichR detail, extent subject quality control/filtering use within package.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"target-disease-associations","dir":"Articles","previous_headings":"Resources - annotation types","what":"Target-disease associations","title":"Annotation resources","text":"Associations genes diseases/tumor types harvested Open Targets Platform. increase confidence target-disease associations shown, include associations support least two data types. weak associations, .e. overall score less 0.05, excluded (complete range 0-1).","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"target-drug-associations","dir":"Articles","previous_headings":"Resources - annotation types","what":"Target-drug associations","title":"Annotation resources","text":"Target-drug associations primarily harvested Open Targets Platform. use phenOncoX R package, dedicated resource phenotype ontology mapping cancer, ensure target-drug associations included oncoEnrichR exclusively cancer conditions.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"tumor-suppressorproto-oncogenecancer-driver-annotation","dir":"Articles","previous_headings":"Resources - annotation types","what":"Tumor suppressor/proto-oncogene/cancer driver annotation","title":"Annotation resources","text":"assign three confidence levels respect genes oncogenic /tumor suppressive roles Strong_support (> 20 citations) biomedical literature (CancerMine), curated entry Network Cancer Genes (NCG) Cancer Gene Census (CGC), Manually curated entry NCG CGC, significant support (> 10 citations) biomedical literature (CancerMine) Curated entry NCG CGC, moderate support (<= 10 citations, > 5 citations) biomedical literature (CancerMine), Significant support (> 10 citations, <= 20 citations) biomedical literature (CancerMine), entry CGC/NCG Curated entry NCG/CGC, weak support (<= 5 citations) biomedical literature (CancerMine), Moderate support (<= 10 citations, > 5 citations) biomedical literature (CancerMine), entry CGC/NCG Literature support tumor suppressive role ignored gene 2.5 times much literature support oncogenic role (vice versa) Classification genes potential cancer drivers require support least two following sources: Network Cancer Genes - canonical cancer drivers IntOGen - predicted cancer driver genes Cancer Gene Census - TIER1/2 - curated cancer genes TCGA’s predicted cancer driver genes CancerMine - literature mining resource, considering entries support > 5 citations)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"gene-cancer-hallmark-associations","dir":"Articles","previous_headings":"Resources - annotation types","what":"Gene cancer hallmark associations","title":"Annotation resources","text":"hallmarks cancer comprise six biological capabilities acquired multistep development human tumors. Genes attributed hallmarks cancer retrieved Open Targets Platform/COSMIC","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"gene-copy-number-aberrations-in-tumors-somatic-amplificationshomozygous-deletions","dir":"Articles","previous_headings":"Resources - annotation types","what":"Gene copy number aberrations in tumors (somatic amplifications/homozygous deletions)","title":"Annotation resources","text":"Somatic copy number amplifications homozygous deletions retrieved Cancer Genome Atlas (TCGA), focusing gene-level calls processed copy number variation analysis pipeline. Copy number events included oncoEnrichR limited high-level amplifications (GISTIC2 CNA value: 2) homozygous deletions (GISTIC2 CNA value: -2)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"recurrent-gene-mutations-in-tumors-somatic-snvsindels","dir":"Articles","previous_headings":"Resources - annotation types","what":"Recurrent gene mutations in tumors (somatic SNVs/InDels)","title":"Annotation resources","text":"Recurrent somatic SNVs/InDels (occurring one tumor sample) retrieved Cancer Genome Atlas (TCGA). SNVs/InDels annotated information mutation hotspots cancer (cancerhotspots.org), protein domains PFAM, predicted status loss--function variants (LOFTEE). protein-altering canonical splice site mutations included.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"gene-co-expression-in-tumors-rna-seq","dir":"Articles","previous_headings":"Resources - annotation types","what":"Gene co-expression in tumors (RNA-seq)","title":"Annotation resources","text":"Co-expression correlation coefficients genes tumors pre-calculated, using RNAseq data available Cancer Genome Atlas (TCGA). calculate separate correlation coefficients tumor type, limit pairs co-expressed genes include either tumor suppressor, oncogene, predicted cancer driver (using classification outlined ). strong correlation coefficients (Spearman’s rank >= 0.7 <= -0.7) included","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"molecular-gene-signatures-pathways","dir":"Articles","previous_headings":"Resources - annotation types","what":"Molecular gene signatures / pathways","title":"Annotation resources","text":"comprehensive set pathway annotations molecular gene signatures form basis functional enrichment module offered oncoEnrichR. include diverse set molecular signatures MSigDB, annotations respect molecular function, biological processes cellular components Gene Ontology (GO), pathway annotations KEGG, WikiPathways, NetPath, Reactome","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"celltissue-specific-gene-expression-patterns","dir":"Articles","previous_headings":"Resources - annotation types","what":"Cell/tissue-specific gene expression patterns","title":"Annotation resources","text":"provide tissue- cell-type specific gene expression annotations Human Protein Atlas. Tissue-specific patterns derived Tissue Atlas, tissue specificity derived deep sequencing RNA (RNA-seq) 50 different normal tissue types. putative protein-coding genes classified respect abundance (tissue enriched, tissue enhanced etc.) different tissues. cell type specificity, utilize single cell RNA (scRNA) sequencing datasets aggregated within Human Protein Atlas. , classification protein-coding genes based single cell type-specific expression 81 different cell types performed; determining types genes elevated (cell type enriched, cell type enhanced etc.) particular cell type compared cell types.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"gene-fitness-effects","dir":"Articles","previous_headings":"Resources - annotation types","what":"Gene fitness effects","title":"Annotation resources","text":"Gene fitness effects retrieved integration data DepMap & Project Score. include data genes statistically significant effect cell fitness cancer cell lines (fitness score considered quantitative measure reduction cell viability elicited gene inactivation, via CRISPR/Cas9 targeting).","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"subcellular-compartment-annotation","dir":"Articles","previous_headings":"Resources - annotation types","what":"Subcellular compartment annotation","title":"Annotation resources","text":"Confidence score target compartment annotation (range 3 5) type channels support annotations ( Knowledge, Text mining Experimental), well required minimum number channels support given target compartment annotation","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"protein-complexes-and-protein-domains","dir":"Articles","previous_headings":"Resources - annotation types","what":"Protein complexes and protein domains","title":"Annotation resources","text":"Protein complex annotations retrieved multiple resources, including CORUM, Compleat, ComplexPortal, hu.MAP2. Protein domains retrieved Pfam","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"protein-protein-interactions","dir":"Articles","previous_headings":"Resources - annotation types","what":"Protein-protein interactions","title":"Annotation resources","text":"Protein-protein interactions members target set explored using data two different resources: required minimum interaction score, limiting interactions retrieved interaction score greater equal threshold. Interaction scores indicators confidence, .e. likely STRING judges interaction true. type network retrieve, either physical functional addition proteins (maximum 50) part query set, interact confidently proteins query set required minimum number evidence items support interaction (.e. multiple types low high-throughput experiments, e.g. affinity capture-MS, affinity capture-Western). Default: 3, maximum: 10 addition proteins (maximum 50) part query set, interact confidently proteins query set","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"gene-regulatory-interactions","dir":"Articles","previous_headings":"Resources - annotation types","what":"Gene regulatory interactions","title":"Annotation resources","text":"Regulatory interactions (TF-target) retrieved DoRothEA resource. Two collections interactions subject overlap query set oncoEnrichR: global set regulatory interactions, many inferred gene expression patterns normal tissues (GTEx), cancer-focused set, latter inferred gene expression patterns tumors (TCGA).","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"prognostic-gene-associations","dir":"Articles","previous_headings":"Resources - annotation types","what":"Prognostic gene associations","title":"Annotation resources","text":"Prognostic associations (gene expression versus survival) collected Human Pathology Atlas, undertaken correlation analyses mRNA expression levels human genes tumor tissue clinical outcome (survival) ~8,000 cancer patients (underlying data TCGA). Correlation analyses resulted 10,000 prognostic genes. show prognostic genes regard cancer type whether favorable unfavorable terms clinical outcome. Furthermore, show prognostic associations established tcga-survival.com, relates various types gene aberrations (expression methylation levels, CNA/mutation status) tumor samples patient survival.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"ligand-receptor-interactions","dir":"Articles","previous_headings":"Resources - annotation types","what":"Ligand-receptor interactions","title":"Annotation resources","text":"Ligand-receptor interactions collected CellChatDB resource. oncoEnrichR module interactions, interactions ligand receptor found query set shown.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/annotation_resources.html","id":"synthetic-lethality-interactions","dir":"Articles","previous_headings":"Resources - annotation types","what":"Synthetic lethality interactions","title":"Annotation resources","text":"Predicted synthetic lethality interactions human gene paralogs collected De Kegel et al., Cell Systems, 2021. Interactions shown members part query set, interactions single member query set present.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/input.html","id":"input-data","dir":"Articles","previous_headings":"","what":"Input data","title":"Input","text":"main input oncoEnrichR list human genes, typically top ranked hits high-throughput screen. gene list can provided using following identifiers: Primary gene symbols (e.g. KRAS) Entrez gene IDs (e.g. 3845) Uniprot accessions (e.g. P01116) Ensembl gene identifiers (e.g. ENSG00000133703) Ensembl transcript identifiers (e.g. ENST00000311936) Ensembl protein identifiers (e.g. ENSP00000308495) RefSeq transcript identifiers (e.g. NM_004985) RefSeq peptide identifiers (e.g. NP_004976) type identifier used specified using --query_id_type argument. Similarly, background gene set specified (--bgset argument, use enrichment analysis), identifier type set --bgset_id_type argument. user submits gene symbols longer considered primary gene symbols, oncoEnrichR attempts map cases synonyms/aliases primary gene symbols.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/input.html","id":"number-of-input-genes","dir":"Articles","previous_headings":"Input data","what":"Number of input genes","title":"Input","text":"order keep size HTML output report manageable level, currently upper limit n = 1000 genes can used input tool. Please also note tool requires n = 2 input genes bare minimum, although analysis modules included/run genes input. IMPORTANT NOTE: Due large size, HTML report can slow load generating full reports maximum number genes (n = 1000). generally recommend use oncoEnrichR smaller querysets (order 100-600), produce reports can efficiently loaded viewed. want submit query pushes limit (n = 1000), recommend carefully configure report contents/modules, sense producing managable reports.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/installation.html","id":"requirementsdependencies","dir":"Articles","previous_headings":"","what":"Requirements/dependencies","title":"Installation","text":"oncoEnrichR requires R (>= version 4.1)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/installation.html","id":"installation-of-oncoenrichr-with-r-commands","dir":"Articles","previous_headings":"","what":"Installation of oncoEnrichR with R commands","title":"Installation","text":"install.packages('remotes') remotes::install_github('sigven/oncoEnrichR', ref = \"v1.4.2\") library(oncoEnrichR)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"output-files","dir":"Articles","previous_headings":"","what":"Output files","title":"Output","text":"output analyses performed oncoEnrichR provided two different formats: interactive HTML report multi-sheet Excel workbook","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"html-report","dir":"Articles","previous_headings":"Output files","what":"HTML report","title":"Output","text":", showcase screenshots oncoEnrichR interactive HTML report, following various types questions can answered tool.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"query-verification","dir":"Articles","previous_headings":"Output files > HTML report","what":"Query verification","title":"Output","text":"gene/query identifiers correctly identified? query identifiers outdated, longer considered primary identifier?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"poorly-characterized-genes","dir":"Articles","previous_headings":"Output files > HTML report","what":"Poorly characterized genes","title":"Output","text":"members query set poorly characterized/unknown function?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"cancer-associations","dir":"Articles","previous_headings":"Output files > HTML report","what":"Cancer associations","title":"Output","text":"tumor types associated genes queryset? extents? genes classified tumor suppressors, proto-oncogenes potential cancer driver genes?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"cancer-hallmark-evidence","dir":"Articles","previous_headings":"Output files > HTML report","what":"Cancer hallmark evidence","title":"Output","text":"genes attributed hallmarks cancer?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"drug-associations","dir":"Articles","previous_headings":"Output files > HTML report","what":"Drug associations","title":"Output","text":"available targeted cancer drugs query set members? cancer indications approved drugs targeted towards query set members? target tractabilities query set members?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"synthetic-lethality","dir":"Articles","previous_headings":"Output files > HTML report","what":"Synthetic lethality","title":"Output","text":"genes predicted take part synthetic lethality interactions?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"gene-fitness-scores","dir":"Articles","previous_headings":"Output files > HTML report","what":"Gene fitness scores","title":"Output","text":"members query set significant effect cell fitness, considering large-scale genome-wide CRISPR–Cas9 dropout screening data cancer cell lines?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"protein-complexes","dir":"Articles","previous_headings":"Output files > HTML report","what":"Protein complexes","title":"Output","text":"members query set involved cancer-relevant protein complexes?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"protein-domains","dir":"Articles","previous_headings":"Output files > HTML report","what":"Protein domains","title":"Output","text":"protein domains frequent among members query set?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"protein-protein-interaction-network","dir":"Articles","previous_headings":"Output files > HTML report","what":"Protein-protein interaction network","title":"Output","text":"protein-protein interactions represented query set? proteins hubs interaction network? members query set form community structures network?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"regulatory-interactions","dir":"Articles","previous_headings":"Output files > HTML report","what":"Regulatory interactions","title":"Output","text":"transcriptional regulatory interactions query set? TF/regulator target present? regulatory targets TFs present? regulators targets?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"subcellular-compartments","dir":"Articles","previous_headings":"Output files > HTML report","what":"Subcellular compartments","title":"Output","text":"subcellular compartments represented query set?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"function-and-pathway-enrichment","dir":"Articles","previous_headings":"Output files > HTML report","what":"Function and pathway enrichment","title":"Output","text":"biological pathways/processes, molecular functions, cancer gene signatures enriched query set?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"tissue-and-cell-type-enrichment","dir":"Articles","previous_headings":"Output files > HTML report","what":"Tissue and cell type enrichment","title":"Output","text":"tissue- cell-type specific expression patterns query genes normal/healthy tissue?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"tumor-aberration-frequencies","dir":"Articles","previous_headings":"Output files > HTML report","what":"Tumor aberration frequencies","title":"Output","text":"extent genes query set mutated tumor samples, copy number alterations point mutations/indels?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"tumor-co-expression","dir":"Articles","previous_headings":"Output files > HTML report","what":"Tumor co-expression","title":"Output","text":"members query set co-expressed cancer genes tumor samples?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"prognostic-associations","dir":"Articles","previous_headings":"Output files > HTML report","what":"Prognostic associations","title":"Output","text":"genes linked survival cancer patients, considering expression methylation levels, mutation status query genes tumor samples?","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/output.html","id":"excel-workbook","dir":"Articles","previous_headings":"Output files","what":"Excel workbook","title":"Output","text":"Excel workbook contains results various analyses conducted, organized multiple sheets (indicated red circles screenshot )","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/running.html","id":"key-functions","dir":"Articles","previous_headings":"","what":"Key functions","title":"Running","text":"oncoEnrichR performs operations following three functions:","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/running.html","id":"oncoenrichrload_db","dir":"Articles","previous_headings":"Key functions","what":"1. oncoEnrichR::load_db()","title":"Running","text":"Loads underlying annotation data repository oncoEnrichR, saves local cache directory. Utilizing googledrive R package","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/running.html","id":"oncoenrichronco_enrich","dir":"Articles","previous_headings":"Key functions","what":"2. oncoEnrichR::onco_enrich()","title":"Running","text":"Consists two main processing steps: 1) Takes input/query list human gene/protein identifiers (e.g. UniProt accession, RefSeq/Ensembl transcript identifer etc.) input conducts uniform identifier conversion 2) Performs extensive annotation, enrichment membership analyses query set underlying data sources cancer-relevant properties human genes interrelationships. Technically, method returns list object contents analyses performed. specific arguments/options default values outlined : See detailed descriptions options ","code":"onco_enrich(   query = NULL,   oeDB = NULL,   query_id_type = \"symbol\",   ignore_id_err = TRUE,   html_floating_toc = T,   html_report_theme = \"default\",   project_title = \"_Project title_\",   project_owner = \"_Project owner_\",   project_description = \"_Project description_\",   bgset = NULL,   bgset_id_type = \"symbol\",   bgset_description = \"All protein-coding genes\",   enrichment_p_value_cutoff = 0.05,   enrichment_p_value_adj = \"BH\",   enrichment_q_value_cutoff = 0.2,   enrichment_min_geneset_size = 10,   enrichment_max_geneset_size = 500,   enrichment_plot_num_terms = 20,   enrichment_simplify_go = TRUE,   subcellcomp_min_confidence = 3,   subcellcomp_min_channels = 1,   subcellcomp_show_cytosol = FALSE,   regulatory_min_confidence = \"D\",   fitness_max_score = -2,   ppi_add_nodes = 30,   ppi_string_min_score = 0.9,   ppi_string_network_type = \"functional\",   ppi_biogrid_min_evidence = 3,   ppi_node_shadow = TRUE,   ppi_show_drugs = TRUE,   ppi_show_isolated_nodes = FALSE,   show_ppi = TRUE,   show_disease = TRUE,   show_top_diseases_only = TRUE,   show_cancer_hallmarks = TRUE,   show_drug = TRUE,   show_enrichment = TRUE,   show_aberration = TRUE,   show_coexpression = TRUE,   show_cell_tissue = FALSE,   show_ligand_receptor = TRUE,   show_regulatory = TRUE,   show_unknown_function = TRUE,   show_prognostic = TRUE,   show_subcell_comp = TRUE,   show_synleth = TRUE,   show_fitness = TRUE,   show_complex = TRUE,   show_domain = TRUE)"},{"path":"https://sigven.github.io/oncoEnrichR/articles/running.html","id":"oncoenrichrwrite","dir":"Articles","previous_headings":"Key functions","what":"3. oncoEnrichR::write()","title":"Running","text":"Consists two main processing steps: 1) Transformation raw analysis results returned oncoEnrichR::onco_enrich() various visualizations interactive tables 2) Assembly generation final analysis report ) structured interactive oncoEnrichR HTML report B) multisheet Excel workbook","code":""},{"path":"https://sigven.github.io/oncoEnrichR/articles/running.html","id":"example-run","dir":"Articles","previous_headings":"","what":"Example run","title":"Running","text":"target list n = 134 high-confidence interacting proteins c-MYC oncoprotein previously identified BioID protein proximity assay standard cell culture tumor xenografts (Dingar et al., J Proteomics, 2015). ran target list oncoEnrichR analysis workflow using following configurations onco_enrich method: project_title = \"cMYC_BioID_screen\" project_owner = \"Raught et al.\" produced following HTML report results. R commands provided reproduce example output. NOTE: Replace “LOCAL_FOLDER” directory local computer: library(oncoEnrichR) myc_interact_targets <- read.csv(system.file(\"extdata\",\"myc_data.csv\", package = \"oncoEnrichR\"), stringsAsFactors = F) oeDB <- oncoEnrichR::load_db(cache_dir = \"LOCAL_FOLDER\") myc_report <- oncoEnrichR::onco_enrich(query = myc_interact_targets$symbol, oeDB = oeDB, show_cell_tissue = T, project_title = \"cMYC_BioID_screen\", project_owner = \"Raught et al.\") oncoEnrichR::write(report = myc_report, oeDB = oeDB, file = \"LOCAL_FOLDER/myc_report_oncoenrichr.html\", format = \"html\") oncoEnrichR::write(report = myc_report, oeDB = oeDB, file = \"LOCAL_FOLDER/myc_report_oncoenrichr.xlsx\", format = \"excel\")","code":""},{"path":"https://sigven.github.io/oncoEnrichR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sigve Nakken. Author, maintainer.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sigve Nakken, Sveinung Gundersen, Fabian L. M. Bernal, Dimitris Polychronopoulos, Eivind Hovig, Jørgen Wesche. Comprehensive interrogation gene lists genome-scale cancer screens oncoEnrichR (2023). Int J Cancer. https://doi.org/10.1002/ijc.34666","code":"@Article{,   title = {Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR},   author = {Sigve Nakken and Sveinung Gundersen and Fabian L. M. Bernal and Dimitris Polychronopoulos and Eivind Hovig and Jørgen Wesche},   year = {2023},   doi = {10.1002/ijc.34666},   url = {https://doi.org/10.1002/ijc.34666},   journal = {Int. J. Cancer}, }"},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"oncoenrichr-","dir":"","previous_headings":"","what":"Cancer-dedicated gene set interpretation","title":"Cancer-dedicated gene set interpretation","text":"oncoEnrichR R package functional interrogation human genesets context cancer. primarily intended exploratory analysis, interpretation, prioritization long gene lists, represent common output many types high-throughput cancer biology screens. oncoEnrichR can used interrogate results e.g. genetic screens (siRNA/CRISPR), protein proximity labeling, transcriptomics (differential expression). tool queries variety high-quality data resources order assemble useful gene annotations analyses interactive report (examples report shown ). Web-based access oncoEnrichR available  https://oncotools.elixir.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"questions-addressed-by-oncoenrichr","dir":"","previous_headings":"","what":"Questions addressed by oncoEnrichR","title":"Cancer-dedicated gene set interpretation","text":"contents analysis report provided oncoEnrichR address following scientific questions given gene list: diseases/tumor types known associated genes query set, extent? genes query set known oncogenic tumor suppressive roles, using evidence biomedical literature curated resources? genes query set attributed cancer hallmark evidence? proteins query sets druggable different cancer conditions (early late clinical development phases)? proteins query set, likelihood druggable? protein complexes involve proteins query set? subcellular compartments (nucleus, cytosol, plasma membrane etc) dominant localizations proteins query set? specific tissues cell types enriched query set, considering tissue/cell-type specific expression patterns target genes? protein-protein interactions known within query set? interactions members query set cancer-relevant proteins (e.g. proto-oncogenes, tumor-suppressors predicted cancer drivers)? proteins constitute hubs protein-protein interaction network? known regulatory interactions (TF-target) found within query set, mode regulation (repressive vs. stimulating)? occurrences known ligand-receptor interactions within query set? specific pathways, biological processes, pre-defined molecular signatures enriched within query set, compared reference/background set? members query set frequently mutated tumor sample cohorts (TCGA, SNVs/InDels, homozygous deletions, copy number amplifications)? members query set co-expressed (strong negative positive correlations) cancer-relevant genes (.e. proto-oncogenes tumor suppressors) tumor sample cohorts (TCGA)? members query set associated better/worse survival different cancers, considering high low gene expression levels, mutation, copy number status tumors? members query set predicted partners synthetic lethality interactions? members query set associated cellular loss--fitness CRISPR/Cas9 whole-genome drop screens cancer cell lines (.e. reduction cell viability elicited gene inactivation)? targets prioritized therapeutic targets, considering fitness effects genomic biomarkers combination? See also output views addresses questions .","code":""},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"news","dir":"","previous_headings":"","what":"News","title":"Cancer-dedicated gene set interpretation","text":"August 16th 2023: 1.4.2 release June 18th 2023: 1.4.1 release February 21st 2023: 1.4.0 release September 27th 2022: 1.3.2 release","code":""},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Cancer-dedicated gene set interpretation","text":"use oncoEnrichR, please cite following publication: Sigve Nakken, Sveinung Gundersen, Fabian L. M. Bernal, Dimitris Polychronopoulos, Eivind Hovig, Jørgen Wesche. Comprehensive interrogation gene lists genome-scale cancer screens oncoEnrichR (2023). Int J Cancer. doi:10.1002/ijc.34666","code":""},{"path":[]},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Cancer-dedicated gene set interpretation","text":"Installation instructions run oncoEnrichR Explore various analysis outputs produced oncoEnrichR Annotation resources available oncoEnrichR","code":""},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"contact","dir":"","previous_headings":"","what":"Contact","title":"Cancer-dedicated gene set interpretation","text":"sigven ifi.uio.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/index.html","id":"funding-and-collaboration","dir":"","previous_headings":"","what":"Funding and Collaboration","title":"Cancer-dedicated gene set interpretation","text":"oncoEnrichR supported Centre Cancer Cell Reprogramming University Oslo/Oslo University Hospital, Elixir Norway (Oslo node).        ","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/gseabase.html","id":null,"dir":"Reference","previous_headings":"","what":"GSEAbase imports — gseabase","title":"GSEAbase imports — gseabase","text":"GSEAbase imports","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/init_report.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that initiates oncoEnrichR report structure — init_report","title":"Function that initiates oncoEnrichR report structure — init_report","text":"Function initiates oncoEnrichR report structure","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/init_report.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that initiates oncoEnrichR report structure — init_report","text":"","code":"init_report(   oeDB,   project_title = \"_Project title_\",   project_owner = \"_Project owner_\",   html_floating_toc = T,   html_report_theme = \"default\",   query_id_type = \"symbol\",   ignore_id_err = TRUE,   project_description = \"_Project description_\",   ppi_string_min_score = 0.9,   ppi_string_network_type = \"functional\",   ppi_biogrid_min_evidence = 3,   ppi_add_nodes = 30,   ppi_show_isolated_nodes = FALSE,   ppi_node_shadow = TRUE,   ppi_show_drugs = T,   bgset_description = \"All annotated protein-coding genes\",   bgset_id_type = \"symbol\",   enrichment_p_value_cutoff = 0.05,   enrichment_p_value_adj = \"BH\",   enrichment_q_value_cutoff = 0.2,   enrichment_min_geneset_size = 10,   enrichment_max_geneset_size = 500,   enrichment_plot_num_terms = 20,   enrichment_simplify_go = F,   subcellcomp_min_confidence = 3,   subcellcomp_min_channels = 1,   subcellcomp_show_cytosol = F,   regulatory_min_confidence = \"D\",   fitness_max_score = -2,   show_ppi = T,   show_disease = T,   show_top_diseases_only = T,   show_cancer_hallmarks = T,   show_drug = T,   show_enrichment = T,   show_aberration = T,   show_coexpression = T,   show_subcell_comp = T,   show_fitness = T,   show_cell_tissue = F,   show_ligand_receptor = T,   show_regulatory = T,   show_unknown_function = T,   show_prognostic = T,   show_synleth = T,   show_complex = T,   show_domain = T )"},{"path":"https://sigven.github.io/oncoEnrichR/reference/init_report.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that initiates oncoEnrichR report structure — init_report","text":"oeDB oncoEnrichR annotation database object project_title project title (title report) project_owner name project owner html_floating_toc logical - float table contents left main document content. floating table contents always visible even document scrolled html_report_theme Bootswatch theme HTML report (\"bootstrap\",\"cerulean\",\"cosmo\",\"default\",\"flatly\",\"journal\",\"lumen\",\"paper\",\"sandstone\",\"simplex\",\"spacelab\",\"united\",\"yeti\") query_id_type character indicating source query (one \"uniprot_acc\", \"symbol\", \"entrezgene\", \"ensembl_gene\",\"ensembl_mrna\",\"refseq_mrna\",\"ensembl_protein\",\"refseq_protein\") ignore_id_err logical indicating analysis continue uknown query identifiers encountered project_description project background information ppi_string_min_score minimum score (0 1) confidence retrieved protein-protein interactions (STRING) ppi_string_network_type STRING network type ('physical' 'functional') ppi_biogrid_min_evidence minimum number evidence items protein-protein interactions shown (BIOGRID) ppi_add_nodes number nodes add target set computing protein-protein interaction network (STRING/BIOGRID) ppi_show_isolated_nodes logical indicating targets/nodes without interactions displayed protein-protein interaction network ppi_node_shadow show shadow nodes displayed PPI network (STRING/BIOGRID) ppi_show_drugs logical indicating targeted drugs (> phase 3) displayed protein-protein interaction network bgset_description character indicating type background (e.g. \"lipid-binding proteins (n = 200)\") bgset_id_type character indicating source query (one \"uniprot_acc\", \"symbol\", \"entrezgene\", \"ensembl_gene\",\"ensembl_mrna\",\"refseq_mrna\",\"ensembl_protein\",\"refseq_protein\") enrichment_p_value_cutoff cutoff p-value enrichment/-representation analysis enrichment_p_value_adj one \"holm\", \"hochberg\", \"hommel\", \"bonferroni\", \"BH\", \"\", \"fdr\", \"none\" enrichment_q_value_cutoff cutoff q-value enrichment analysis enrichment_min_geneset_size minimal size geneset annotated term testing enrichment/-representation analysis enrichment_max_geneset_size maximal size geneset annotated term testing enrichment/-representation analysis enrichment_plot_num_terms number top enriched Gene Ontology terms (max) show enrichment barplot enrichment_simplify_go remove highly similar GO terms results GO enrichment/-representation analysis subcellcomp_min_confidence minimun confidence level subcellular compartment annotation COMPARTMENTS (min = 3, max = 5) subcellcomp_min_channels minimum number channels support subcellular annotation COMPARTMENTS subcellcomp_show_cytosol logical indicating subcellular heatmap highlight cytosol subcellular protein location regulatory_min_confidence minimum confidence level regulatory interactions (TF-target) retrieved DoRothEA ('','B','C', 'D') fitness_max_score maximum loss--fitness score (scaled Bayes factor BAGEL) genes retrieved Project Score show_ppi logical indicating report contain protein-protein interaction data (STRING) show_disease logical indicating report contain disease associations (Open Targets Platform, association_score >= 0.05, support least two data types) show_top_diseases_only logical indicating report contain top (n = 20) disease associations pr. query gene (Open Targets Platform) show_cancer_hallmarks logical indicating report contain annotations/evidence cancer hallmarks per query gene (COSMIC/Open Targets Platform) show_drug logical indicating report contain targeted cancer drug information show_enrichment logical indicating report contain functional enrichment/-representation analysis (MSigDB, GO, KEGG, REACTOME, NetPath, WikiPathways) show_aberration logical indicating report contain TCGA aberration plots (amplifications/deletions) show_coexpression logical indicating report contain TCGA co-expression data (RNAseq) query set oncogenes/tumor suppressor genes show_subcell_comp logical indicating report provide subcellular compartment annotations (COMPARTMENTS) show_fitness logical indicating report provide fitness scores target priority scores CRISPR/Cas9 loss--fitness screens (Project Score) show_cell_tissue logical indicating report contain tissue-specificity single cell-type specificity assessments (Human Protein Atlas) target genes, using data Human Protein Atlas show_ligand_receptor logical indicating report contain ligand-receptor interactions (CellChatDB) show_regulatory logical indicating report contain data transcription factor (TF) - target interactions relevant query set (DoRothEA) show_unknown_function logical indicating report highlight target genes unknown poorly defined functions (GO/Uniprot KB/NCBI) show_prognostic logical indicating mRNA-based (single-gene) prognostic associations cancer types listed (Human Protein Atlas/TCGA) show_synleth logical indicating report list overlap predicted synthetic lethality interactions (gene paralogs , De Kegel et al., Cell Systems, 2021) show_complex logical indicating report provide target memberships known protein complexes (ComplexPortal/Compleat/PDB/CORUM) show_domain logical indicating report provide target memberships known protein domains (Pfam)","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/load_db.html","id":null,"dir":"Reference","previous_headings":"","what":"Load oncoEnrichR data repository — load_db","title":"Load oncoEnrichR data repository — load_db","text":"Function fetches version-tagged oncoEnrichR data repository Google Drive","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/load_db.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load oncoEnrichR data repository — load_db","text":"","code":"load_db(cache_dir = NA, force_download = FALSE, googledrive = TRUE)"},{"path":"https://sigven.github.io/oncoEnrichR/reference/load_db.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load oncoEnrichR data repository — load_db","text":"cache_dir Local directory data download force_download Logical indicating local cache force download (.e. set TRUE re-download even data exists cache) googledrive logical indicating use googledrive UiO server host downloading","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/load_db.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load oncoEnrichR data repository — load_db","text":"list object oncoEnrichR datasets, used oeDB argument onco_enrich() write()","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/onco_enrich.html","id":null,"dir":"Reference","previous_headings":"","what":"Interrogate a gene list for cancer relevance — onco_enrich","title":"Interrogate a gene list for cancer relevance — onco_enrich","text":"Function interrogates list human gene identifiers cancer relevance. Multiple perspectives offered, including tumor aberration co-expression patterns, druggability, protein-protein interactions, gene fitness effects, regulatory interactions, subcellular compartment enrichment, pathway enrichment, synthetic lethality interactions, prognostic associations, .","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/onco_enrich.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Interrogate a gene list for cancer relevance — onco_enrich","text":"","code":"onco_enrich(   query = NULL,   oeDB = NULL,   query_id_type = \"symbol\",   ignore_id_err = TRUE,   html_floating_toc = T,   html_report_theme = \"default\",   project_title = \"_Project title_\",   project_owner = \"_Project owner_\",   project_description = \"_Project description_\",   bgset = NULL,   bgset_id_type = \"symbol\",   bgset_description = \"All protein-coding genes\",   enrichment_p_value_cutoff = 0.05,   enrichment_p_value_adj = \"BH\",   enrichment_q_value_cutoff = 0.2,   enrichment_min_geneset_size = 10,   enrichment_max_geneset_size = 500,   enrichment_plot_num_terms = 20,   enrichment_simplify_go = TRUE,   subcellcomp_min_confidence = 3,   subcellcomp_min_channels = 1,   subcellcomp_show_cytosol = FALSE,   regulatory_min_confidence = \"D\",   fitness_max_score = -2,   ppi_add_nodes = 30,   ppi_string_min_score = 0.9,   ppi_string_network_type = \"functional\",   ppi_biogrid_min_evidence = 3,   ppi_node_shadow = TRUE,   ppi_show_drugs = TRUE,   ppi_show_isolated_nodes = FALSE,   show_ppi = TRUE,   show_disease = TRUE,   show_top_diseases_only = TRUE,   show_cancer_hallmarks = TRUE,   show_drug = TRUE,   show_enrichment = TRUE,   show_aberration = TRUE,   show_coexpression = TRUE,   show_cell_tissue = FALSE,   show_ligand_receptor = TRUE,   show_regulatory = TRUE,   show_unknown_function = TRUE,   show_prognostic = TRUE,   show_subcell_comp = TRUE,   show_synleth = TRUE,   show_fitness = TRUE,   show_complex = TRUE,   show_domain = TRUE,   ... )"},{"path":"https://sigven.github.io/oncoEnrichR/reference/onco_enrich.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Interrogate a gene list for cancer relevance — onco_enrich","text":"query character vector gene/query identifiers (minimum 2, maximum 1000) oeDB oncoEnrichR data repository object - returned load_db() query_id_type character indicating source query (one \"uniprot_acc\", \"symbol\",\"entrezgene\", \"ensembl_gene\", \"ensembl_mrna\", \"refseq_mrna\", \"ensembl_protein\", \"refseq_protein\") ignore_id_err logical indicating analysis continue uknown query identifiers encountered html_floating_toc logical - float table contents left main document content (HTML report). floating table contents always visible even document scrolled html_report_theme Bootswatch theme HTML report (\"bootstrap\", \"cerulean\", \"cosmo\", \"default\", \"flatly\", \"journal\", \"lumen\", \"paper\", \"sandstone\", \"simplex\", \"spacelab\", \"united\", \"yeti\") project_title project title (title report) project_owner name project owner project_description project background information bgset character vector gene identifiers, used reference/background enrichment/-representation analysis bgset_id_type character indicating source background (\"uniprot_acc\", \"symbol\", \"entrezgene\", \"ensembl_gene\", \"ensembl_mrna\", \"refseq_mrna\", \"ensembl_protein\", \"refseq_protein\"), default: \"symbol\" bgset_description character indicating type background (e.g. \"lipid-binding proteins (n = 200)\") enrichment_p_value_cutoff cutoff p-value enrichment/ -representation analysis (default: 0.05) enrichment_p_value_adj one \"holm\", \"hochberg\", \"hommel\", \"bonferroni\", \"BH\", \"\", \"fdr\", \"none\" (clusterProfiler, default: \"BH\") enrichment_q_value_cutoff cutoff q-value enrichment analysis (clusterProfiler, default: 0.2) enrichment_min_geneset_size minimal size geneset annotated term testing enrichment/-representation analysis (clusterProfiler, default: 10) enrichment_max_geneset_size maximal size geneset annotated term testing enrichment/-representation analysis (clusterProfiler, default: 500) enrichment_plot_num_terms number top enriched Gene Ontology terms (max) show enrichment barplot (default: 15) enrichment_simplify_go remove highly similar GO terms results GO enrichment/-representation analysis (default: TRUE) subcellcomp_min_confidence minimum confidence level subcellular compartment annotation COMPARTMENTS (min = 3, max = 5, default: 3) subcellcomp_min_channels minimum number channels support subcellular compartment annotation COMPARTMENTS (min = 1, max = 3, default: 1) subcellcomp_show_cytosol logical indicating subcellular heatmap show highlight proteins located cytosol (default: FALSE) regulatory_min_confidence minimum confidence level regulatory interactions (TF-target) retrieved DoRothEA ('','B','C', 'D', default: 'D') fitness_max_score maximum loss--fitness score (scaled Bayes factor BAGEL) genes retrieved DepMap/Project Score, default:-2 ppi_add_nodes number nodes add target set computing protein-protein interaction network (STRING/BioGRID, default: 30) ppi_string_min_score minimum score (0 1) confidence retrieved protein-protein interactions (STRING, default: 0.9) ppi_string_network_type type network show interactions STRING ('functional' 'physical', default: 'functional') ppi_biogrid_min_evidence minimum number evidence items required protein-protein interactions retrieved (BioGRID, default: 3) ppi_node_shadow show shadow nodes displayed PPI network (default: TRUE) ppi_show_drugs logical indicating targeted drugs (>= phase 3) displayed protein-protein interaction networks (default: TRUE) ppi_show_isolated_nodes logical indicating targets/nodes without interactions displayed protein-protein interaction networks (default: FALSE) show_ppi logical indicating report contain protein-protein interaction views query set (STRING BioGRID, default: TRUE) show_disease logical indicating report contain disease associations (Open Targets Platform, association_score >= 0.05, support least two data types), tumor suppressor/oncogene annotations ( default: TRUE) show_top_diseases_only logical indicating report contain top (n = 20) disease associations pr. query gene default: TRUE) show_cancer_hallmarks logical indicating report contain annotations/evidence cancer hallmarks per query gene (COSMIC/Open Targets Platform, default: TRUE show_drug logical indicating report contain targeted cancer drug information (default: TRUE) show_enrichment logical indicating report contain functional enrichment/-representation analysis (MSigDB, GO, KEGG, REACTOME, NetPath, WikiPathways, default: TRUE) show_aberration logical indicating report contain TCGA aberration plots (amplifications/deletions, default: TRUE) show_coexpression logical indicating report contain TCGA co-expression data (RNAseq) query set oncogenes/tumor suppressor genes (default: TRUE) show_cell_tissue logical indicating report contain tissue-specificity single cell-type specificity assessments (Human Protein Atlas) target genes (default: FALSE) show_ligand_receptor logical indicating report contain ligand-receptor interactions (CellChatDB, default: TRUE) show_regulatory logical indicating report contain data transcription factor (TF) - target interactions relevant query set (DoRothEA, default: TRUE) show_unknown_function logical indicating report highlight target genes unknown poorly defined functions (GO/Uniprot KB/NCBI, default: TRUE) show_prognostic logical indicating mRNA-based (single-gene) prognostic associations cancer types listed (Human Protein Atlas/TCGA, default: TRUE show_subcell_comp logical indicating report provide subcellular compartment annotations (COMPARTMENTS, default: TRUE) show_synleth logical indicating report list overlap predicted synthetic lethality interactions (gene paralogs , De Kegel et al., Cell Systems, 2021). Default: TRUE show_fitness logical indicating report provide fitness scores target priority scores CRISPR/Cas9 loss--fitness screens (DepMap/Project Score, default: TRUE) show_complex logical indicating report provide target memberships known protein complexes (ComplexPortal/Compleat/hu.MAP2/PDB/CORUM, default: TRUE) show_domain logical indicating report provide target memberships known protein domains (Pfam, default: TRUE) ... arguments Galaxy/web-based processing","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/onco_enrich.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Interrogate a gene list for cancer relevance — onco_enrich","text":"oncoEnrichR report list object, two main elements, data config. data contains data goes section output reports, config contains metadata annotation resources used.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/tidyeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy eval helpers — tidyeval","title":"Tidy eval helpers — tidyeval","text":"https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that validates the oncoEnrichR database object — validate_db","title":"Function that validates the oncoEnrichR database object — validate_db","text":"Function validates oncoEnrichR database object","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that validates the oncoEnrichR database object — validate_db","text":"","code":"validate_db(oe_db)"},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that validates the oncoEnrichR database object — validate_db","text":"db list object annotation data oncoEnrichR","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that validates a particular db object (data.frame) in oncoEnrichR — validate_db_df","title":"Function that validates a particular db object (data.frame) in oncoEnrichR — validate_db_df","text":"Function validates particular db object (data.frame) oncoEnrichR","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that validates a particular db object (data.frame) in oncoEnrichR — validate_db_df","text":"","code":"validate_db_df(df, dbtype = \"genedb\")"},{"path":"https://sigven.github.io/oncoEnrichR/reference/validate_db_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that validates a particular db object (data.frame) in oncoEnrichR — validate_db_df","text":"df data.frame annotation data oncoEnrichR dbtype type oncoEnrichR datasource","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/write.html","id":null,"dir":"Reference","previous_headings":"","what":"Write oncoEnrichR report object to output file — write","title":"Write oncoEnrichR report object to output file — write","text":"Function writes oncoEnrichR report object file, either interactive HTML report Excel workbook.","code":""},{"path":"https://sigven.github.io/oncoEnrichR/reference/write.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write oncoEnrichR report object to output file — write","text":"","code":"write(   report,   oeDB,   file = \"testReport.html\",   ignore_file_extension = F,   overwrite = F,   format = \"html\",   ... )"},{"path":"https://sigven.github.io/oncoEnrichR/reference/write.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write oncoEnrichR report object to output file — write","text":"report object oncoEnrichR report data (returned oeDB$onco_enrich) oeDB oncoEnrichR data repository object - returned load_db() file full filename report output (e.g. \"oe_report.html\" \"oe_report.xlsx\") ignore_file_extension logical accept type filaname extensions (Galaxy integration) overwrite logical indicating existing output files may overwritten format file format output (html/excel) ... options Galaxy/non self-contained HTML. applicable use Galaxy","code":""}]
diff --git a/sitemap.xml b/sitemap.xml
index 98ad514..611a87e 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -57,9 +57,6 @@
   <url>
     <loc>https://sigven.github.io/oncoEnrichR/reference/tidyeval.html</loc>
   </url>
-  <url>
-    <loc>https://sigven.github.io/oncoEnrichR/reference/url_exists.html</loc>
-  </url>
   <url>
     <loc>https://sigven.github.io/oncoEnrichR/reference/validate_db.html</loc>
   </url>
