diff --git a/404.html b/404.html
index abe5f0e..9491980 100644
--- a/404.html
+++ b/404.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -102,7 +102,7 @@ <h1>Page not found (404)</h1>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+<p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index ef0cb66..154f13e 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -88,7 +88,7 @@ <h1>NA</h1>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html
index 4aee3cb..b49ecf7 100644
--- a/CONTRIBUTING.html
+++ b/CONTRIBUTING.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -104,7 +104,7 @@ <h2 id="code-of-conduct">Code of Conduct<a class="anchor" aria-label="anchor" hr
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/SUPPORT.html b/SUPPORT.html
index d6e3929..0ce0bb4 100644
--- a/SUPPORT.html
+++ b/SUPPORT.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -94,7 +94,7 @@ <h2 id="what-happens-next">What happens next?<a class="anchor" aria-label="ancho
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/articles/header.html b/articles/header.html
index c39d017..41061e8 100644
--- a/articles/header.html
+++ b/articles/header.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -94,7 +94,7 @@ <h4 data-toc-skip class="author">Kevin
 Oxford<br><a class="author_email" href="mailto:#"></a><a href="mailto:kevin.rue-albrecht@imm.ox.ac.uk" class="email">kevin.rue-albrecht@imm.ox.ac.uk</a>
       </address>
                   
-            <h4 data-toc-skip class="date">6 July 2023</h4>
+            <h4 data-toc-skip class="date">22 February 2024</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/iSEE/iSEEindex/blob/HEAD/vignettes/header.Rmd" class="external-link"><code>vignettes/header.Rmd</code></a></small>
       <div class="hidden name"><code>header.Rmd</code></div>
@@ -109,7 +109,7 @@ <h2 id="custom-header-and-footer">Custom header and footer<a class="anchor" aria
 <div class="section level3">
 <h3 id="overview">Overview<a class="anchor" aria-label="anchor" href="#overview"></a>
 </h3>
-<p>By default, <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<p>By default, <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 creates a minimal landing page presenting users with a fluid row that
 contains two <code><a href="https://rdrr.io/pkg/shinydashboard/man/box.html" class="external-link">shinydashboard::box()</a></code>:</p>
 <ul>
@@ -117,7 +117,7 @@ <h3 id="overview">Overview<a class="anchor" aria-label="anchor" href="#overview"
 <li>On the right, users can select an initial configuration and launch
 the main app interface.</li>
 </ul>
-<p><em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<p><em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 offers the opportunity for app maintainers to add content above (i.e.,
 header) and below (i.e., footer) that row.</p>
 <p>That header and footer space may contain any valid UI element that
@@ -205,12 +205,12 @@ <h2 id="example">Example<a class="anchor" aria-label="anchor" href="#example"></
 <div class="section level2">
 <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" href="#reproducibility"></a>
 </h2>
-<p>The <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
-package (Rue-Albrecht, 2022) was made possible thanks to:</p>
+<p>The <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
+package (Rue-Albrecht and Marini, 2024) was made possible thanks to:</p>
 <ul>
-<li>R (R Core Team, 2023)</li>
+<li>R (R Core Team, 2024)</li>
 <li>
-<em><a href="https://bioconductor.org/packages/3.17/BiocStyle" class="external-link">BiocStyle</a></em>
+<em><a href="https://bioconductor.org/packages/3.19/BiocStyle" class="external-link">BiocStyle</a></em>
 (Oleś, 2023)</li>
 <li>
 <em><a href="https://CRAN.R-project.org/package=knitr" class="external-link">knitr</a></em> (Xie,
@@ -229,7 +229,7 @@ <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" hr
 <em><a href="https://CRAN.R-project.org/package=testthat" class="external-link">testthat</a></em>
 (Wickham, 2011)</li>
 </ul>
-<p>This package was developed using <em><a href="https://bioconductor.org/packages/3.17/biocthis" class="external-link">biocthis</a></em>.</p>
+<p>This package was developed using <em><a href="https://bioconductor.org/packages/3.19/biocthis" class="external-link">biocthis</a></em>.</p>
 <p>Code for creating the vignette</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co">## Create the vignette</span></span>
@@ -240,155 +240,156 @@ <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" hr
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://yihui.org/knitr/" class="external-link">"knitr"</a></span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/knit.html" class="external-link">knit</a></span><span class="op">(</span><span class="st">"header.Rmd"</span>, tangle <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
 <p>Date the vignette was generated.</p>
-<pre><code><span><span class="co">#&gt; [1] "2023-07-06 20:01:50 UTC"</span></span></code></pre>
+<pre><code><span><span class="co">#&gt; [1] "2024-02-22 12:57:06 UTC"</span></span></code></pre>
 <p>Wallclock time spent generating the vignette.</p>
-<pre><code><span><span class="co">#&gt; Time difference of 8.535 secs</span></span></code></pre>
+<pre><code><span><span class="co">#&gt; Time difference of 7.44 secs</span></span></code></pre>
 <p><code>R</code> session information.</p>
 <pre><code><span><span class="co">#&gt; <span style="color: #00BBBB; font-weight: bold;">─ Session info ───────────────────────────────────────────────────────────────────────────────────</span></span></span>
 <span><span class="co">#&gt;  <span style="color: #555555; font-style: italic;">setting </span> <span style="color: #555555; font-style: italic;">value</span></span></span>
-<span><span class="co">#&gt;  version  R version 4.3.1 (2023-06-16)</span></span>
-<span><span class="co">#&gt;  os       Ubuntu 22.04.2 LTS</span></span>
+<span><span class="co">#&gt;  version  R Under development (unstable) (2024-02-19 r85946)</span></span>
+<span><span class="co">#&gt;  os       Ubuntu 22.04.3 LTS</span></span>
 <span><span class="co">#&gt;  system   x86_64, linux-gnu</span></span>
 <span><span class="co">#&gt;  ui       X11</span></span>
 <span><span class="co">#&gt;  language en</span></span>
 <span><span class="co">#&gt;  collate  en_US.UTF-8</span></span>
 <span><span class="co">#&gt;  ctype    en_US.UTF-8</span></span>
 <span><span class="co">#&gt;  tz       UTC</span></span>
-<span><span class="co">#&gt;  date     2023-07-06</span></span>
+<span><span class="co">#&gt;  date     2024-02-22</span></span>
 <span><span class="co">#&gt;  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB; font-weight: bold;">─ Packages ───────────────────────────────────────────────────────────────────────────────────────</span></span></span>
 <span><span class="co">#&gt;  <span style="color: #555555; font-style: italic;">package             </span> <span style="color: #555555; font-style: italic;">*</span> <span style="color: #555555; font-style: italic;">version  </span> <span style="color: #555555; font-style: italic;">date (UTC)</span> <span style="color: #555555; font-style: italic;">lib</span> <span style="color: #555555; font-style: italic;">source</span></span></span>
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-<span><span class="co">#&gt;  GlobalOptions          0.1.2     <span style="color: #555555;">2020-06-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  glue                   1.6.2     <span style="color: #555555;">2022-02-24</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  gtable                 0.3.3     <span style="color: #555555;">2023-03-21</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  highr                  0.10      <span style="color: #555555;">2022-12-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  htmltools              0.5.5     <span style="color: #555555;">2023-03-23</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  htmlwidgets            1.6.2     <span style="color: #555555;">2023-03-17</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  httpuv                 1.6.11    <span style="color: #555555;">2023-05-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  httr                   1.4.6     <span style="color: #555555;">2023-05-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  igraph                 1.5.0     <span style="color: #555555;">2023-06-16</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  IRanges              * 2.34.1    <span style="color: #555555;">2023-06-22</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  iSEE                   2.12.0    <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  iSEEindex            * 0.99.13   <span style="color: #555555;">2023-07-06</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  iterators              1.0.14    <span style="color: #555555;">2022-02-05</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  jquerylib              0.1.4     <span style="color: #555555;">2021-04-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  jsonlite               1.8.7     <span style="color: #555555;">2023-06-29</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  knitr                  1.43      <span style="color: #555555;">2023-05-25</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  later                  1.3.1     <span style="color: #555555;">2023-05-02</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  lattice                0.21-8    <span style="color: #555555;">2023-04-05</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  lifecycle              1.0.3     <span style="color: #555555;">2022-10-07</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  lubridate              1.9.2     <span style="color: #555555;">2023-02-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  magrittr               2.0.3     <span style="color: #555555;">2022-03-30</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  Matrix                 1.5-4.1   <span style="color: #555555;">2023-05-18</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  MatrixGenerics       * 1.12.2    <span style="color: #555555;">2023-06-09</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  matrixStats          * 1.0.0     <span style="color: #555555;">2023-06-02</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  memoise                2.0.1     <span style="color: #555555;">2021-11-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  mgcv                   1.8-42    <span style="color: #555555;">2023-03-02</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  mime                   0.12      <span style="color: #555555;">2021-09-28</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  miniUI                 0.1.1.1   <span style="color: #555555;">2018-05-18</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  munsell                0.5.0     <span style="color: #555555;">2018-06-12</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  nlme                   3.1-162   <span style="color: #555555;">2023-01-31</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  paws.common            0.5.8     <span style="color: #555555;">2023-07-06</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  paws.storage           0.3.0     <span style="color: #555555;">2023-06-22</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  pillar                 1.9.0     <span style="color: #555555;">2023-03-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  pkgconfig              2.0.3     <span style="color: #555555;">2019-09-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  pkgdown                2.0.7     <span style="color: #555555;">2022-12-14</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  plyr                   1.8.8     <span style="color: #555555;">2022-11-11</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  png                    0.1-8     <span style="color: #555555;">2022-11-29</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  promises               1.2.0.1   <span style="color: #555555;">2021-02-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  purrr                  1.0.1     <span style="color: #555555;">2023-01-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  R6                     2.5.1     <span style="color: #555555;">2021-08-19</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  ragg                   1.2.5     <span style="color: #555555;">2023-01-12</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  RColorBrewer           1.1-3     <span style="color: #555555;">2022-04-03</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  Rcpp                   1.0.11    <span style="color: #555555;">2023-07-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  RCurl                  1.98-1.12 <span style="color: #555555;">2023-03-27</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  RefManageR           * 1.4.0     <span style="color: #555555;">2022-09-30</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rintrojs               0.3.2     <span style="color: #555555;">2022-08-09</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rjson                  0.2.21    <span style="color: #555555;">2022-01-09</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rlang                  1.1.1     <span style="color: #555555;">2023-04-28</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rmarkdown              2.23      <span style="color: #555555;">2023-07-01</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rprojroot              2.0.3     <span style="color: #555555;">2022-04-02</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  RSQLite                2.3.1     <span style="color: #555555;">2023-04-03</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  S4Arrays               1.0.4     <span style="color: #555555;">2023-05-14</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  S4Vectors            * 0.38.1    <span style="color: #555555;">2023-05-02</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  sass                   0.4.6     <span style="color: #555555;">2023-05-03</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  scales                 1.2.1     <span style="color: #555555;">2022-08-20</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  sessioninfo          * 1.2.2     <span style="color: #555555;">2021-12-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shape                  1.4.6     <span style="color: #555555;">2021-05-19</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shiny                * 1.7.4.1   <span style="color: #555555;">2023-07-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shinyAce               0.4.2     <span style="color: #555555;">2022-05-06</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shinydashboard         0.7.2     <span style="color: #555555;">2021-09-30</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shinyjs                2.1.0     <span style="color: #555555;">2021-12-23</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shinyWidgets           0.7.6     <span style="color: #555555;">2023-01-08</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  SingleCellExperiment * 1.22.0    <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  stringi                1.7.12    <span style="color: #555555;">2023-01-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  stringr                1.5.0     <span style="color: #555555;">2022-12-02</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  SummarizedExperiment * 1.30.2    <span style="color: #555555;">2023-06-06</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  systemfonts            1.0.4     <span style="color: #555555;">2022-02-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  textshaping            0.3.6     <span style="color: #555555;">2021-10-13</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  tibble                 3.2.1     <span style="color: #555555;">2023-03-20</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  tidyselect             1.2.0     <span style="color: #555555;">2022-10-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  timechange             0.2.0     <span style="color: #555555;">2023-01-11</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  triebeard              0.4.1     <span style="color: #555555;">2023-03-04</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  urltools               1.7.3     <span style="color: #555555;">2019-04-14</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  utf8                   1.2.3     <span style="color: #555555;">2023-01-31</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  vctrs                  0.6.3     <span style="color: #555555;">2023-06-14</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  vipor                  0.4.5     <span style="color: #555555;">2017-03-22</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  viridisLite            0.4.2     <span style="color: #555555;">2023-05-02</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  xfun                   0.39      <span style="color: #555555;">2023-04-20</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  xml2                   1.3.5     <span style="color: #555555;">2023-07-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  xtable                 1.8-4     <span style="color: #555555;">2019-04-21</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  XVector                0.40.0    <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  yaml                   2.3.7     <span style="color: #555555;">2023-01-23</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  zlibbioc               1.46.0    <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  abind                  1.4-5     <span style="color: #555555;">2016-07-21</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  backports              1.4.1     <span style="color: #555555;">2021-12-13</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bibtex                 0.5.1     <span style="color: #555555;">2023-01-26</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  Biobase              * 2.63.0    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  BiocFileCache        * 2.11.1    <span style="color: #555555;">2023-10-26</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  BiocGenerics         * 0.49.1    <span style="color: #555555;">2023-11-01</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  BiocManager            1.30.22   <span style="color: #555555;">2023-08-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  BiocStyle            * 2.31.0    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  bit                    4.0.5     <span style="color: #555555;">2022-11-15</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bit64                  4.0.5     <span style="color: #555555;">2020-08-30</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bitops                 1.0-7     <span style="color: #555555;">2021-04-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  blob                   1.2.4     <span style="color: #555555;">2023-03-17</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bookdown               0.37      <span style="color: #555555;">2023-12-01</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bslib                  0.6.1     <span style="color: #555555;">2023-11-28</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  cachem                 1.0.8     <span style="color: #555555;">2023-05-01</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  circlize               0.4.16    <span style="color: #555555;">2024-02-20</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  cli                    3.6.2     <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  clue                   0.3-65    <span style="color: #555555;">2023-09-23</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  cluster                2.1.6     <span style="color: #555555;">2023-12-01</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  codetools              0.2-19    <span style="color: #555555;">2023-02-01</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  colorspace             2.1-0     <span style="color: #555555;">2023-01-23</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  colourpicker           1.3.0     <span style="color: #555555;">2023-08-21</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  ComplexHeatmap         2.19.0    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  crayon                 1.5.2     <span style="color: #555555;">2022-09-29</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  curl                   5.2.0     <span style="color: #555555;">2023-12-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  DBI                    1.2.2     <span style="color: #555555;">2024-02-16</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  dbplyr               * 2.4.0     <span style="color: #555555;">2023-10-26</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  DelayedArray           0.29.4    <span style="color: #555555;">2024-02-19</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor 3.19 (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  desc                   1.4.3     <span style="color: #555555;">2023-12-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  digest                 0.6.34    <span style="color: #555555;">2024-01-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  doParallel             1.0.17    <span style="color: #555555;">2022-02-07</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  dplyr                  1.1.4     <span style="color: #555555;">2023-11-17</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
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+<span><span class="co">#&gt;  ellipsis               0.3.2     <span style="color: #555555;">2021-04-29</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  evaluate               0.23      <span style="color: #555555;">2023-11-01</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  fansi                  1.0.6     <span style="color: #555555;">2023-12-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  fastmap                1.1.1     <span style="color: #555555;">2023-02-24</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
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+<span><span class="co">#&gt;  fontawesome            0.5.2     <span style="color: #555555;">2023-08-19</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  foreach                1.5.2     <span style="color: #555555;">2022-02-02</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  fs                     1.6.3     <span style="color: #555555;">2023-07-20</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  generics               0.1.3     <span style="color: #555555;">2022-07-05</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  GenomeInfoDb         * 1.39.6    <span style="color: #555555;">2024-02-08</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor 3.19 (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  GenomeInfoDbData       1.2.11    <span style="color: #555555;">2024-02-04</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  GenomicRanges        * 1.55.3    <span style="color: #555555;">2024-02-13</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor 3.19 (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  GetoptLong             1.0.5     <span style="color: #555555;">2020-12-15</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  ggplot2                3.4.4     <span style="color: #555555;">2023-10-12</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  ggrepel                0.9.5     <span style="color: #555555;">2024-01-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  GlobalOptions          0.1.2     <span style="color: #555555;">2020-06-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  glue                   1.7.0     <span style="color: #555555;">2024-01-09</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  gtable                 0.3.4     <span style="color: #555555;">2023-08-21</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  highr                  0.10      <span style="color: #555555;">2022-12-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  htmltools              0.5.7     <span style="color: #555555;">2023-11-03</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  htmlwidgets            1.6.4     <span style="color: #555555;">2023-12-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  httpuv                 1.6.14    <span style="color: #555555;">2024-01-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  httr                   1.4.7     <span style="color: #555555;">2023-08-15</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  igraph                 2.0.2     <span style="color: #555555;">2024-02-17</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  IRanges              * 2.37.1    <span style="color: #555555;">2024-01-19</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor 3.19 (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  iSEE                   2.15.0    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  iSEEindex            * 1.1.1     <span style="color: #555555;">2024-02-22</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  iterators              1.0.14    <span style="color: #555555;">2022-02-05</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  jquerylib              0.1.4     <span style="color: #555555;">2021-04-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  jsonlite               1.8.8     <span style="color: #555555;">2023-12-04</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  knitr                  1.45      <span style="color: #555555;">2023-10-30</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  later                  1.3.2     <span style="color: #555555;">2023-12-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  lattice                0.22-5    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  lifecycle              1.0.4     <span style="color: #555555;">2023-11-07</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  lubridate              1.9.3     <span style="color: #555555;">2023-09-27</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  magrittr               2.0.3     <span style="color: #555555;">2022-03-30</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  Matrix                 1.6-5     <span style="color: #555555;">2024-01-11</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  MatrixGenerics       * 1.15.0    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  matrixStats          * 1.2.0     <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  memoise                2.0.1     <span style="color: #555555;">2021-11-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  mgcv                   1.9-1     <span style="color: #555555;">2023-12-21</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  mime                   0.12      <span style="color: #555555;">2021-09-28</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  miniUI                 0.1.1.1   <span style="color: #555555;">2018-05-18</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  munsell                0.5.0     <span style="color: #555555;">2018-06-12</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  nlme                   3.1-164   <span style="color: #555555;">2023-11-27</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  paws.common            0.7.0     <span style="color: #555555;">2024-01-09</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  paws.storage           0.5.0     <span style="color: #555555;">2024-01-09</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  pillar                 1.9.0     <span style="color: #555555;">2023-03-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  pkgconfig              2.0.3     <span style="color: #555555;">2019-09-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  pkgdown                2.0.7     <span style="color: #555555;">2022-12-14</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  plyr                   1.8.9     <span style="color: #555555;">2023-10-02</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  png                    0.1-8     <span style="color: #555555;">2022-11-29</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  promises               1.2.1     <span style="color: #555555;">2023-08-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  purrr                  1.0.2     <span style="color: #555555;">2023-08-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  R6                     2.5.1     <span style="color: #555555;">2021-08-19</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  ragg                   1.2.7     <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  RColorBrewer           1.1-3     <span style="color: #555555;">2022-04-03</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  Rcpp                   1.0.12    <span style="color: #555555;">2024-01-09</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  RCurl                  1.98-1.14 <span style="color: #555555;">2024-01-09</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  RefManageR           * 1.4.0     <span style="color: #555555;">2022-09-30</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  rintrojs               0.3.4     <span style="color: #555555;">2024-01-11</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  rjson                  0.2.21    <span style="color: #555555;">2022-01-09</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  rlang                  1.1.3     <span style="color: #555555;">2024-01-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  rmarkdown              2.25      <span style="color: #555555;">2023-09-18</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  RSQLite                2.3.5     <span style="color: #555555;">2024-01-21</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  S4Arrays               1.3.3     <span style="color: #555555;">2024-01-31</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor 3.19 (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  S4Vectors            * 0.41.3    <span style="color: #555555;">2024-01-01</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor 3.19 (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  sass                   0.4.8     <span style="color: #555555;">2023-12-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  scales                 1.3.0     <span style="color: #555555;">2023-11-28</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  sessioninfo          * 1.2.2     <span style="color: #555555;">2021-12-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  shape                  1.4.6     <span style="color: #555555;">2021-05-19</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  shiny                * 1.8.0     <span style="color: #555555;">2023-11-17</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
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+<span><span class="co">#&gt;  shinydashboard         0.7.2     <span style="color: #555555;">2021-09-30</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  shinyjs                2.1.0     <span style="color: #555555;">2021-12-23</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  shinyWidgets           0.8.1     <span style="color: #555555;">2024-01-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  SingleCellExperiment * 1.25.0    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  SparseArray            1.3.4     <span style="color: #555555;">2024-02-11</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor 3.19 (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  stringi                1.8.3     <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  stringr                1.5.1     <span style="color: #555555;">2023-11-14</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  SummarizedExperiment * 1.33.3    <span style="color: #555555;">2024-01-23</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor 3.19 (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  systemfonts            1.0.5     <span style="color: #555555;">2023-10-09</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  textshaping            0.3.7     <span style="color: #555555;">2023-10-09</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  tibble                 3.2.1     <span style="color: #555555;">2023-03-20</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  tidyselect             1.2.0     <span style="color: #555555;">2022-10-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  timechange             0.3.0     <span style="color: #555555;">2024-01-18</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  triebeard              0.4.1     <span style="color: #555555;">2023-03-04</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  urltools               1.7.3     <span style="color: #555555;">2019-04-14</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  utf8                   1.2.4     <span style="color: #555555;">2023-10-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  vctrs                  0.6.5     <span style="color: #555555;">2023-12-01</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  vipor                  0.4.7     <span style="color: #555555;">2023-12-18</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  viridisLite            0.4.2     <span style="color: #555555;">2023-05-02</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  xfun                   0.42      <span style="color: #555555;">2024-02-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  xml2                   1.3.6     <span style="color: #555555;">2023-12-04</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  xtable                 1.8-4     <span style="color: #555555;">2019-04-21</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  XVector                0.43.1    <span style="color: #555555;">2024-01-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor 3.19 (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  yaml                   2.3.8     <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  zlibbioc               1.49.0    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; <span style="color: #555555;"> [1] /__w/_temp/Library</span></span></span>
 <span><span class="co">#&gt; <span style="color: #555555;"> [2] /usr/local/lib/R/site-library</span></span></span>
@@ -399,7 +400,7 @@ <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" hr
 <div class="section level2">
 <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#bibliography"></a>
 </h2>
-<p>This vignette was generated using <em><a href="https://bioconductor.org/packages/3.17/BiocStyle" class="external-link">BiocStyle</a></em>
+<p>This vignette was generated using <em><a href="https://bioconductor.org/packages/3.19/BiocStyle" class="external-link">BiocStyle</a></em>
 (Oleś, 2023) with <em><a href="https://CRAN.R-project.org/package=knitr" class="external-link">knitr</a></em> (Xie,
 2023) and <em><a href="https://CRAN.R-project.org/package=rmarkdown" class="external-link">rmarkdown</a></em>
 (Allaire, Xie, Dervieux et al., 2023) running behind the scenes.</p>
@@ -408,7 +409,7 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 <p>
 <a id="bib-allaire2023rmarkdown"></a><a href="#cite-allaire2023rmarkdown">[1]</a><cite>
 J. Allaire, Y. Xie, C. Dervieux, et al. <em>rmarkdown: Dynamic Documents
-for R</em>. R package version 2.23. 2023. URL:
+for R</em>. R package version 2.25. 2023. URL:
 <a href="https://github.com/rstudio/rmarkdown" class="external-link">https://github.com/rstudio/rmarkdown</a>.</cite>
 </p>
 <p>
@@ -421,23 +422,23 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 <p>
 <a id="bib-ole2023biocstyle"></a><a href="#cite-ole2023biocstyle">[3]</a><cite>
 A. Oleś. <em>BiocStyle: Standard styles for vignettes and other
-Bioconductor documents</em>. R package version 2.28.0. 2023. DOI:
+Bioconductor documents</em>. R package version 2.31.0. 2023. DOI:
 <a href="https://doi.org/10.18129/B9.bioc.BiocStyle" class="external-link">10.18129/B9.bioc.BiocStyle</a>.
 URL:
 <a href="https://bioconductor.org/packages/BiocStyle" class="external-link">https://bioconductor.org/packages/BiocStyle</a>.</cite>
 </p>
 <p>
-<a id="bib-2023language"></a><a href="#cite-2023language">[4]</a><cite>
+<a id="bib-2024language"></a><a href="#cite-2024language">[4]</a><cite>
 R Core Team. <em>R: A Language and Environment for Statistical
 Computing</em>. R Foundation for Statistical Computing. Vienna, Austria,
-2023. URL:
+2024. URL:
 <a href="https://www.R-project.org/" class="external-link">https://www.R-project.org/</a>.</cite>
 </p>
 <p>
-<a id="bib-ruealbrecht2022iseeindex"></a><a href="#cite-ruealbrecht2022iseeindex">[5]</a><cite>
-K. Rue-Albrecht. <em>iSEEindex: iSEE extension for a landing page to a
-custom collection of data sets</em>. R package version 0.99.13. 2022.
-URL:
+<a id="bib-ruealbrecht2024iseeindex"></a><a href="#cite-ruealbrecht2024iseeindex">[5]</a><cite>
+K. Rue-Albrecht and F. Marini. <em>iSEEindex: iSEE extension for a
+landing page to a custom collection of data sets</em>. R package version
+1.1.1. 2024. URL:
 <a href="https://github.com/iSEE/iSEEindex" class="external-link">https://github.com/iSEE/iSEEindex</a>.</cite>
 </p>
 <p>
@@ -455,7 +456,7 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 <p>
 <a id="bib-xie2023knitr"></a><a href="#cite-xie2023knitr">[8]</a><cite>
 Y. Xie. <em>knitr: A General-Purpose Package for Dynamic Report
-Generation in R</em>. R package version 1.43. 2023. URL:
+Generation in R</em>. R package version 1.45. 2023. URL:
 <a href="https://yihui.org/knitr/" class="external-link">https://yihui.org/knitr/</a>.</cite>
 </p>
 <!-- Links -->
@@ -474,7 +475,7 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+<p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/articles/iSEEindex.html b/articles/iSEEindex.html
index 0f8af16..99e6bba 100644
--- a/articles/iSEEindex.html
+++ b/articles/iSEEindex.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -93,7 +93,7 @@ <h4 data-toc-skip class="author">Kevin
 Oxford<br><a class="author_email" href="mailto:#"></a><a href="mailto:kevin.rue-albrecht@imm.ox.ac.uk" class="email">kevin.rue-albrecht@imm.ox.ac.uk</a>
       </address>
                   
-            <h4 data-toc-skip class="date">6 July 2023</h4>
+            <h4 data-toc-skip class="date">22 February 2024</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/iSEE/iSEEindex/blob/HEAD/vignettes/iSEEindex.Rmd" class="external-link"><code>vignettes/iSEEindex.Rmd</code></a></small>
       <div class="hidden name"><code>iSEEindex.Rmd</code></div>
@@ -109,10 +109,10 @@ <h2 id="basics">Basics<a class="anchor" aria-label="anchor" href="#basics"></a>
 <h3 id="install-iseeindex">Install <code>iSEEindex</code><a class="anchor" aria-label="anchor" href="#install-iseeindex"></a>
 </h3>
 <p><code>R</code> is an open-source statistical environment which can be
-easily modified to enhance its functionality via packages. <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+easily modified to enhance its functionality via packages. <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 is a <code>R</code> package available via the <a href="http://bioconductor.org" class="external-link">Bioconductor</a> repository for packages.
 <code>R</code> can be installed on any operating system from <a href="https://cran.r-project.org/" class="external-link">CRAN</a> after which you can install
-<em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 by using the following commands in your <code>R</code> session:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"BiocManager"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
@@ -127,13 +127,13 @@ <h3 id="install-iseeindex">Install <code>iSEEindex</code><a class="anchor" aria-
 <div class="section level3">
 <h3 id="required-knowledge">Required knowledge<a class="anchor" aria-label="anchor" href="#required-knowledge"></a>
 </h3>
-<p><em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<p><em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 is based on many other packages and in particular those that have
 implemented the infrastructure needed for dealing with omics data and
-interactive visualisation. That is, packages like <em><a href="https://bioconductor.org/packages/3.17/SummarizedExperiment" class="external-link">SummarizedExperiment</a></em>,
-<em><a href="https://bioconductor.org/packages/3.17/SingleCellExperiment" class="external-link">SingleCellExperiment</a></em>,
-<em><a href="https://bioconductor.org/packages/3.17/iSEE" class="external-link">iSEE</a></em>
-and <em><a href="https://bioconductor.org/packages/3.17/shiny" class="external-link">shiny</a></em>.</p>
+interactive visualisation. That is, packages like <em><a href="https://bioconductor.org/packages/3.19/SummarizedExperiment" class="external-link">SummarizedExperiment</a></em>,
+<em><a href="https://bioconductor.org/packages/3.19/SingleCellExperiment" class="external-link">SingleCellExperiment</a></em>,
+<em><a href="https://bioconductor.org/packages/3.19/iSEE" class="external-link">iSEE</a></em>
+and <em><a href="https://bioconductor.org/packages/3.19/shiny" class="external-link">shiny</a></em>.</p>
 <p>If you are asking yourself the question “Where do I start using
 Bioconductor?” you might be interested in <a href="http://lcolladotor.github.io/2014/10/16/startbioc/#.VkOKbq6rRuU" class="external-link">this
 blog post</a>.</p>
@@ -158,7 +158,7 @@ <h3 id="asking-for-help">Asking for help<a class="anchor" aria-label="anchor" hr
 <div class="section level3">
 <h3 id="citing-iseeindex">Citing <code>iSEEindex</code><a class="anchor" aria-label="anchor" href="#citing-iseeindex"></a>
 </h3>
-<p>We hope that <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<p>We hope that <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 will be useful for your research. Please use the following information
 to cite the package and the overall approach. Thank you!</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
@@ -166,17 +166,17 @@ <h3 id="citing-iseeindex">Citing <code>iSEEindex</code><a class="anchor" aria-la
 <span><span class="fu"><a href="https://rdrr.io/r/utils/citation.html" class="external-link">citation</a></span><span class="op">(</span><span class="st">"iSEEindex"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; To cite package 'iSEEindex' in publications use:</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt;   Rue-Albrecht K (2022). _iSEEindex: iSEE extension for a landing page</span></span>
-<span><span class="co">#&gt;   to a custom collection of data sets_. R package version 0.99.13,</span></span>
-<span><span class="co">#&gt;   &lt;https://github.com/iSEE/iSEEindex&gt;.</span></span>
+<span><span class="co">#&gt;   Rue-Albrecht K, Marini F (2024). _iSEEindex: iSEE extension for a</span></span>
+<span><span class="co">#&gt;   landing page to a custom collection of data sets_. R package version</span></span>
+<span><span class="co">#&gt;   1.1.1, &lt;https://github.com/iSEE/iSEEindex&gt;.</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; A BibTeX entry for LaTeX users is</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt;   @Manual{,</span></span>
 <span><span class="co">#&gt;     title = {iSEEindex: iSEE extension for a landing page to a custom collection of data sets},</span></span>
-<span><span class="co">#&gt;     author = {Kevin Rue-Albrecht},</span></span>
-<span><span class="co">#&gt;     year = {2022},</span></span>
-<span><span class="co">#&gt;     note = {R package version 0.99.13},</span></span>
+<span><span class="co">#&gt;     author = {Kevin Rue-Albrecht and Federico Marini},</span></span>
+<span><span class="co">#&gt;     year = {2024},</span></span>
+<span><span class="co">#&gt;     note = {R package version 1.1.1},</span></span>
 <span><span class="co">#&gt;     url = {https://github.com/iSEE/iSEEindex},</span></span>
 <span><span class="co">#&gt;   }</span></span></code></pre></div>
 </div>
@@ -209,9 +209,9 @@ <h2 id="quick-start-to-using-iseeindex">Quick start to using <code>iSEEindex</co
 <span><span class="op">}</span></span></code></pre></div>
 <p><img src="screenshots/landing_page.png" width="600"></p>
 <p>Let’s break down this example step by step, to illustrate the
-functionality and flexibility of <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>.</p>
-<p>First, we load the <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
-and <em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>
+functionality and flexibility of <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>.</p>
+<p>First, we load the <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
+and <em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>
 packages, to access their functionality.</p>
 <p>Next, we use the <code><a href="https://rdrr.io/pkg/BiocFileCache/man/BiocFileCache-class.html" class="external-link">BiocFileCache::BiocFileCache()</a></code>
 function, to create a persistent on-disk cache of files that the app can
@@ -240,7 +240,7 @@ <h2 id="quick-start-to-using-iseeindex">Quick start to using <code>iSEEindex</co
 <code><a href="../reference/iSEEindex.html">?iSEEindex</a></code>, for the argument <code>FUN.initial</code>.</p>
 <p>Then, we pass the <code>BiocFileCache</code> object and the two
 custom functions defined above to the
-<code><a href="../reference/iSEEindex.html">iSEEindex::iSEEindex()</a></code> function, to create an <em><a href="https://bioconductor.org/packages/3.17/iSEE" class="external-link">iSEE</a></em>
+<code><a href="../reference/iSEEindex.html">iSEEindex::iSEEindex()</a></code> function, to create an <em><a href="https://bioconductor.org/packages/3.19/iSEE" class="external-link">iSEE</a></em>
 application that incorporates a landing page offering users the choice
 of data sets and initial configurations fetched by the custom
 functions.</p>
@@ -250,12 +250,12 @@ <h2 id="quick-start-to-using-iseeindex">Quick start to using <code>iSEEindex</co
 <div class="section level2">
 <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" href="#reproducibility"></a>
 </h2>
-<p>The <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
-package (Rue-Albrecht, 2022) was made possible thanks to:</p>
+<p>The <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
+package (Rue-Albrecht and Marini, 2024) was made possible thanks to:</p>
 <ul>
-<li>R (R Core Team, 2023)</li>
+<li>R (R Core Team, 2024)</li>
 <li>
-<em><a href="https://bioconductor.org/packages/3.17/BiocStyle" class="external-link">BiocStyle</a></em>
+<em><a href="https://bioconductor.org/packages/3.19/BiocStyle" class="external-link">BiocStyle</a></em>
 (Oleś, 2023)</li>
 <li>
 <em><a href="https://CRAN.R-project.org/package=knitr" class="external-link">knitr</a></em> (Xie,
@@ -274,7 +274,7 @@ <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" hr
 <em><a href="https://CRAN.R-project.org/package=testthat" class="external-link">testthat</a></em>
 (Wickham, 2011)</li>
 </ul>
-<p>This package was developed using <em><a href="https://bioconductor.org/packages/3.17/biocthis" class="external-link">biocthis</a></em>.</p>
+<p>This package was developed using <em><a href="https://bioconductor.org/packages/3.19/biocthis" class="external-link">biocthis</a></em>.</p>
 <p>Code for creating the vignette</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co">## Create the vignette</span></span>
@@ -285,155 +285,156 @@ <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" hr
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://yihui.org/knitr/" class="external-link">"knitr"</a></span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/knit.html" class="external-link">knit</a></span><span class="op">(</span><span class="st">"iSEEindex.Rmd"</span>, tangle <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
 <p>Date the vignette was generated.</p>
-<pre><code><span><span class="co">#&gt; [1] "2023-07-06 20:02:04 UTC"</span></span></code></pre>
+<pre><code><span><span class="co">#&gt; [1] "2024-02-22 12:57:18 UTC"</span></span></code></pre>
 <p>Wallclock time spent generating the vignette.</p>
-<pre><code><span><span class="co">#&gt; Time difference of 8.62 secs</span></span></code></pre>
+<pre><code><span><span class="co">#&gt; Time difference of 7.624 secs</span></span></code></pre>
 <p><code>R</code> session information.</p>
 <pre><code><span><span class="co">#&gt; <span style="color: #00BBBB; font-weight: bold;">─ Session info ───────────────────────────────────────────────────────────────────────────────────</span></span></span>
 <span><span class="co">#&gt;  <span style="color: #555555; font-style: italic;">setting </span> <span style="color: #555555; font-style: italic;">value</span></span></span>
-<span><span class="co">#&gt;  version  R version 4.3.1 (2023-06-16)</span></span>
-<span><span class="co">#&gt;  os       Ubuntu 22.04.2 LTS</span></span>
+<span><span class="co">#&gt;  version  R Under development (unstable) (2024-02-19 r85946)</span></span>
+<span><span class="co">#&gt;  os       Ubuntu 22.04.3 LTS</span></span>
 <span><span class="co">#&gt;  system   x86_64, linux-gnu</span></span>
 <span><span class="co">#&gt;  ui       X11</span></span>
 <span><span class="co">#&gt;  language en</span></span>
 <span><span class="co">#&gt;  collate  en_US.UTF-8</span></span>
 <span><span class="co">#&gt;  ctype    en_US.UTF-8</span></span>
 <span><span class="co">#&gt;  tz       UTC</span></span>
-<span><span class="co">#&gt;  date     2023-07-06</span></span>
+<span><span class="co">#&gt;  date     2024-02-22</span></span>
 <span><span class="co">#&gt;  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB; font-weight: bold;">─ Packages ───────────────────────────────────────────────────────────────────────────────────────</span></span></span>
 <span><span class="co">#&gt;  <span style="color: #555555; font-style: italic;">package             </span> <span style="color: #555555; font-style: italic;">*</span> <span style="color: #555555; font-style: italic;">version  </span> <span style="color: #555555; font-style: italic;">date (UTC)</span> <span style="color: #555555; font-style: italic;">lib</span> <span style="color: #555555; font-style: italic;">source</span></span></span>
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-<span><span class="co">#&gt;  fansi                  1.0.4     <span style="color: #555555;">2023-01-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  fastmap                1.1.1     <span style="color: #555555;">2023-02-24</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  fontawesome            0.5.1     <span style="color: #555555;">2023-04-18</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  fs                     1.6.2     <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  generics               0.1.3     <span style="color: #555555;">2022-07-05</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  GenomeInfoDb         * 1.36.1    <span style="color: #555555;">2023-06-21</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  GenomeInfoDbData       1.2.10    <span style="color: #555555;">2023-07-05</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  GenomicRanges        * 1.52.0    <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  GetoptLong             1.0.5     <span style="color: #555555;">2020-12-15</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  ggplot2                3.4.2     <span style="color: #555555;">2023-04-03</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  ggrepel                0.9.3     <span style="color: #555555;">2023-02-03</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  GlobalOptions          0.1.2     <span style="color: #555555;">2020-06-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  glue                   1.6.2     <span style="color: #555555;">2022-02-24</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  gtable                 0.3.3     <span style="color: #555555;">2023-03-21</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  highr                  0.10      <span style="color: #555555;">2022-12-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  htmltools              0.5.5     <span style="color: #555555;">2023-03-23</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  htmlwidgets            1.6.2     <span style="color: #555555;">2023-03-17</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  httpuv                 1.6.11    <span style="color: #555555;">2023-05-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  jquerylib              0.1.4     <span style="color: #555555;">2021-04-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  jsonlite               1.8.7     <span style="color: #555555;">2023-06-29</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  knitr                  1.43      <span style="color: #555555;">2023-05-25</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  lattice                0.21-8    <span style="color: #555555;">2023-04-05</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  paws.storage           0.3.0     <span style="color: #555555;">2023-06-22</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  pillar                 1.9.0     <span style="color: #555555;">2023-03-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  pkgconfig              2.0.3     <span style="color: #555555;">2019-09-22</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  pkgdown                2.0.7     <span style="color: #555555;">2022-12-14</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  plyr                   1.8.8     <span style="color: #555555;">2022-11-11</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  png                    0.1-8     <span style="color: #555555;">2022-11-29</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  promises               1.2.0.1   <span style="color: #555555;">2021-02-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  purrr                  1.0.1     <span style="color: #555555;">2023-01-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  R6                     2.5.1     <span style="color: #555555;">2021-08-19</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  ragg                   1.2.5     <span style="color: #555555;">2023-01-12</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  RColorBrewer           1.1-3     <span style="color: #555555;">2022-04-03</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  Rcpp                   1.0.11    <span style="color: #555555;">2023-07-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  RCurl                  1.98-1.12 <span style="color: #555555;">2023-03-27</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  RefManageR           * 1.4.0     <span style="color: #555555;">2022-09-30</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rintrojs               0.3.2     <span style="color: #555555;">2022-08-09</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rjson                  0.2.21    <span style="color: #555555;">2022-01-09</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rlang                  1.1.1     <span style="color: #555555;">2023-04-28</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rmarkdown              2.23      <span style="color: #555555;">2023-07-01</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rprojroot              2.0.3     <span style="color: #555555;">2022-04-02</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  RSQLite                2.3.1     <span style="color: #555555;">2023-04-03</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  S4Arrays               1.0.4     <span style="color: #555555;">2023-05-14</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  S4Vectors            * 0.38.1    <span style="color: #555555;">2023-05-02</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  sass                   0.4.6     <span style="color: #555555;">2023-05-03</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  scales                 1.2.1     <span style="color: #555555;">2022-08-20</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  sessioninfo          * 1.2.2     <span style="color: #555555;">2021-12-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shape                  1.4.6     <span style="color: #555555;">2021-05-19</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shiny                  1.7.4.1   <span style="color: #555555;">2023-07-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shinyAce               0.4.2     <span style="color: #555555;">2022-05-06</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shinydashboard         0.7.2     <span style="color: #555555;">2021-09-30</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shinyjs                2.1.0     <span style="color: #555555;">2021-12-23</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  shinyWidgets           0.7.6     <span style="color: #555555;">2023-01-08</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  SingleCellExperiment * 1.22.0    <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  stringi                1.7.12    <span style="color: #555555;">2023-01-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  stringr                1.5.0     <span style="color: #555555;">2022-12-02</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  SummarizedExperiment * 1.30.2    <span style="color: #555555;">2023-06-06</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  systemfonts            1.0.4     <span style="color: #555555;">2022-02-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  textshaping            0.3.6     <span style="color: #555555;">2021-10-13</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  tibble                 3.2.1     <span style="color: #555555;">2023-03-20</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  tidyselect             1.2.0     <span style="color: #555555;">2022-10-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  timechange             0.2.0     <span style="color: #555555;">2023-01-11</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  triebeard              0.4.1     <span style="color: #555555;">2023-03-04</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  urltools               1.7.3     <span style="color: #555555;">2019-04-14</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  utf8                   1.2.3     <span style="color: #555555;">2023-01-31</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  vctrs                  0.6.3     <span style="color: #555555;">2023-06-14</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  vipor                  0.4.5     <span style="color: #555555;">2017-03-22</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  viridisLite            0.4.2     <span style="color: #555555;">2023-05-02</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  xfun                   0.39      <span style="color: #555555;">2023-04-20</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  xml2                   1.3.5     <span style="color: #555555;">2023-07-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  xtable                 1.8-4     <span style="color: #555555;">2019-04-21</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  XVector                0.40.0    <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  yaml                   2.3.7     <span style="color: #555555;">2023-01-23</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  zlibbioc               1.46.0    <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  abind                  1.4-5     <span style="color: #555555;">2016-07-21</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  backports              1.4.1     <span style="color: #555555;">2021-12-13</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bibtex                 0.5.1     <span style="color: #555555;">2023-01-26</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  Biobase              * 2.63.0    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  BiocFileCache        * 2.11.1    <span style="color: #555555;">2023-10-26</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  BiocGenerics         * 0.49.1    <span style="color: #555555;">2023-11-01</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  BiocManager            1.30.22   <span style="color: #555555;">2023-08-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  BiocStyle            * 2.31.0    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  bit                    4.0.5     <span style="color: #555555;">2022-11-15</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bit64                  4.0.5     <span style="color: #555555;">2020-08-30</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bitops                 1.0-7     <span style="color: #555555;">2021-04-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  blob                   1.2.4     <span style="color: #555555;">2023-03-17</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bookdown               0.37      <span style="color: #555555;">2023-12-01</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bslib                  0.6.1     <span style="color: #555555;">2023-11-28</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  cachem                 1.0.8     <span style="color: #555555;">2023-05-01</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  circlize               0.4.16    <span style="color: #555555;">2024-02-20</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  cli                    3.6.2     <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  clue                   0.3-65    <span style="color: #555555;">2023-09-23</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  cluster                2.1.6     <span style="color: #555555;">2023-12-01</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  codetools              0.2-19    <span style="color: #555555;">2023-02-01</span> <span style="color: #555555;">[3]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  colorspace             2.1-0     <span style="color: #555555;">2023-01-23</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  colourpicker           1.3.0     <span style="color: #555555;">2023-08-21</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  ComplexHeatmap         2.19.0    <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  crayon                 1.5.2     <span style="color: #555555;">2022-09-29</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  curl                   5.2.0     <span style="color: #555555;">2023-12-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  DBI                    1.2.2     <span style="color: #555555;">2024-02-16</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  dbplyr               * 2.4.0     <span style="color: #555555;">2023-10-26</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  DelayedArray           0.29.4    <span style="color: #555555;">2024-02-19</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor 3.19 (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  desc                   1.4.3     <span style="color: #555555;">2023-12-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  digest                 0.6.34    <span style="color: #555555;">2024-01-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  doParallel             1.0.17    <span style="color: #555555;">2022-02-07</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  dplyr                  1.1.4     <span style="color: #555555;">2023-11-17</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  DT                     0.32      <span style="color: #555555;">2024-02-19</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  ellipsis               0.3.2     <span style="color: #555555;">2021-04-29</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  evaluate               0.23      <span style="color: #555555;">2023-11-01</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  fansi                  1.0.6     <span style="color: #555555;">2023-12-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  fastmap                1.1.1     <span style="color: #555555;">2023-02-24</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  filelock               1.0.3     <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  fontawesome            0.5.2     <span style="color: #555555;">2023-08-19</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  foreach                1.5.2     <span style="color: #555555;">2022-02-02</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  fs                     1.6.3     <span style="color: #555555;">2023-07-20</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
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@@ -444,7 +445,7 @@ <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" hr
 <div class="section level2">
 <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#bibliography"></a>
 </h2>
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+<p>This vignette was generated using <em><a href="https://bioconductor.org/packages/3.19/BiocStyle" class="external-link">BiocStyle</a></em>
 (Oleś, 2023) with <em><a href="https://CRAN.R-project.org/package=knitr" class="external-link">knitr</a></em> (Xie,
 2023) and <em><a href="https://CRAN.R-project.org/package=rmarkdown" class="external-link">rmarkdown</a></em>
 (Allaire, Xie, Dervieux et al., 2023) running behind the scenes.</p>
@@ -453,7 +454,7 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 <p>
 <a id="bib-allaire2023rmarkdown"></a><a href="#cite-allaire2023rmarkdown">[1]</a><cite>
 J. Allaire, Y. Xie, C. Dervieux, et al. <em>rmarkdown: Dynamic Documents
-for R</em>. R package version 2.23. 2023. URL:
+for R</em>. R package version 2.25. 2023. URL:
 <a href="https://github.com/rstudio/rmarkdown" class="external-link">https://github.com/rstudio/rmarkdown</a>.</cite>
 </p>
 <p>
@@ -466,23 +467,23 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 <p>
 <a id="bib-ole2023biocstyle"></a><a href="#cite-ole2023biocstyle">[3]</a><cite>
 A. Oleś. <em>BiocStyle: Standard styles for vignettes and other
-Bioconductor documents</em>. R package version 2.28.0. 2023. DOI:
+Bioconductor documents</em>. R package version 2.31.0. 2023. DOI:
 <a href="https://doi.org/10.18129/B9.bioc.BiocStyle" class="external-link">10.18129/B9.bioc.BiocStyle</a>.
 URL:
 <a href="https://bioconductor.org/packages/BiocStyle" class="external-link">https://bioconductor.org/packages/BiocStyle</a>.</cite>
 </p>
 <p>
-<a id="bib-2023language"></a><a href="#cite-2023language">[4]</a><cite>
+<a id="bib-2024language"></a><a href="#cite-2024language">[4]</a><cite>
 R Core Team. <em>R: A Language and Environment for Statistical
 Computing</em>. R Foundation for Statistical Computing. Vienna, Austria,
-2023. URL:
+2024. URL:
 <a href="https://www.R-project.org/" class="external-link">https://www.R-project.org/</a>.</cite>
 </p>
 <p>
-<a id="bib-ruealbrecht2022iseeindex"></a><a href="#cite-ruealbrecht2022iseeindex">[5]</a><cite>
-K. Rue-Albrecht. <em>iSEEindex: iSEE extension for a landing page to a
-custom collection of data sets</em>. R package version 0.99.13. 2022.
-URL:
+<a id="bib-ruealbrecht2024iseeindex"></a><a href="#cite-ruealbrecht2024iseeindex">[5]</a><cite>
+K. Rue-Albrecht and F. Marini. <em>iSEEindex: iSEE extension for a
+landing page to a custom collection of data sets</em>. R package version
+1.1.1. 2024. URL:
 <a href="https://github.com/iSEE/iSEEindex" class="external-link">https://github.com/iSEE/iSEEindex</a>.</cite>
 </p>
 <p>
@@ -500,7 +501,7 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 <p>
 <a id="bib-xie2023knitr"></a><a href="#cite-xie2023knitr">[8]</a><cite>
 Y. Xie. <em>knitr: A General-Purpose Package for Dynamic Report
-Generation in R</em>. R package version 1.43. 2023. URL:
+Generation in R</em>. R package version 1.45. 2023. URL:
 <a href="https://yihui.org/knitr/" class="external-link">https://yihui.org/knitr/</a>.</cite>
 </p>
 <!-- Links -->
@@ -519,7 +520,7 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+<p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/articles/index.html b/articles/index.html
index f3a5f85..54e53dd 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -78,7 +78,7 @@ <h3>All vignettes</h3>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/articles/resources.html b/articles/resources.html
index 1e690bf..153ae46 100644
--- a/articles/resources.html
+++ b/articles/resources.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -93,7 +93,7 @@ <h4 data-toc-skip class="author">Kevin
 Oxford<br><a class="author_email" href="mailto:#"></a><a href="mailto:kevin.rue-albrecht@imm.ox.ac.uk" class="email">kevin.rue-albrecht@imm.ox.ac.uk</a>
       </address>
                   
-            <h4 data-toc-skip class="date">6 July 2023</h4>
+            <h4 data-toc-skip class="date">22 February 2024</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/iSEE/iSEEindex/blob/HEAD/vignettes/resources.Rmd" class="external-link"><code>vignettes/resources.Rmd</code></a></small>
       <div class="hidden name"><code>resources.Rmd</code></div>
@@ -108,34 +108,34 @@ <h2 id="iseeindex-resources">iSEEindex resources<a class="anchor" aria-label="an
 <div class="section level3">
 <h3 id="overview">Overview<a class="anchor" aria-label="anchor" href="#overview"></a>
 </h3>
-<p><em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<p><em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 imports data sets and initial app configurations from files. Each of
 those files is represented by a Uniform Resource Identifier (URI) in the
 lists of metadata returned by the functions supplied to the
 <code>FUN.datasets</code> and <code>FUN.initial</code> arguments of
 <code><a href="../reference/iSEEindex.html">iSEEindex()</a></code>.</p>
-<p><em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<p><em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 requires each URI to contain a scheme component (<a href="https://en.wikipedia.org/wiki/Uniform_Resource_Identifier#Syntax" class="external-link">Wikipedia</a>
 <svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M320 0c-17.7 0-32 14.3-32 32s14.3 32 32 32h82.7L201.4 265.4c-12.5 12.5-12.5 32.8 0 45.3s32.8 12.5 45.3 0L448 109.3V192c0 17.7 14.3 32 32 32s32-14.3 32-32V32c0-17.7-14.3-32-32-32H320zM80 32C35.8 32 0 67.8 0 112V432c0 44.2 35.8 80 80 80H400c44.2 0 80-35.8 80-80V320c0-17.7-14.3-32-32-32s-32 14.3-32 32V432c0 8.8-7.2 16-16 16H80c-8.8 0-16-7.2-16-16V112c0-8.8 7.2-16 16-16H192c17.7 0 32-14.3 32-32s-14.3-32-32-32H80z"></path></svg>),
 to identify the type of resource and invoke the associated method for
 accessing it.</p>
-<p>This system allows <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<p>This system allows <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 users to use both standard and custom schemes in the URI of their
 resources, to fetch files from virtually any logical or physical
 resource, local or remote.</p>
-<p>In this vignette, we describe the implementation of <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<p>In this vignette, we describe the implementation of <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 resources, using built-in classes of resources as examples.</p>
 </div>
 <div class="section level3">
 <h3 id="implementation">Implementation<a class="anchor" aria-label="anchor" href="#implementation"></a>
 </h3>
-<p>Given a scheme <code>&lt;scheme&gt;</code>, <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<p>Given a scheme <code>&lt;scheme&gt;</code>, <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 automatically attempts to create an object of class
 <code>iSEEindex&lt;Scheme&gt;Resource</code> that contains the class
 <code>iSEEindexResource</code>. For instance, the scheme
 <code>https</code> produces an object of class
 <code>iSEEindexHttpsResource</code>.</p>
-<p><em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
+<p><em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
 provides a range of built-in <code>iSEEindexResource</code> sub-classes,
 described in <a href="#builtin">dedicated sections below</a>.</p>
 <p>The raw value of the URI (including the scheme component) is always
@@ -145,9 +145,9 @@ <h3 id="implementation">Implementation<a class="anchor" aria-label="anchor" href
 <code><a href="../reference/iSEEindexResource-generics.html">precache()</a></code>.</p>
 <p>On first use, <code><a href="../reference/iSEEindexResource-generics.html">precache()</a></code> processes the raw value of the
 URI, downloads the resource file locally using custom code if necessary,
-caches the file using <em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>,
+caches the file using <em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>,
 and returns the path to the cached file.</p>
-<p>In subsequent uses, <em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>
+<p>In subsequent uses, <em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>
 is used to fetch the cached file directly.</p>
 </div>
 </div>
@@ -172,10 +172,10 @@ <h4 id="structure">Structure<a class="anchor" aria-label="anchor" href="#structu
 <div class="section level4">
 <h4 id="caching">Caching<a class="anchor" aria-label="anchor" href="#caching"></a>
 </h4>
-<p>The <em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>
+<p>The <em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>
 package can handle HTTPS perfectly well.</p>
 <p>In this instance, the <code><a href="../reference/iSEEindexResource-generics.html">precache()</a></code> function has no other
-job than to cache the file located at the given URI using <em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>.</p>
+job than to cache the file located at the given URI using <em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>.</p>
 </div>
 </div>
 <div class="section level3">
@@ -197,12 +197,12 @@ <h4 id="structure-1">Structure<a class="anchor" aria-label="anchor" href="#struc
 <div class="section level4">
 <h4 id="caching-1">Caching<a class="anchor" aria-label="anchor" href="#caching-1"></a>
 </h4>
-<p>Now, while the <em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>
+<p>Now, while the <em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>
 package can perfectly well handle local files, it does not know how to
 deal with the custom scheme <code>localhost</code>.</p>
 <p>In this instance, the <code><a href="../reference/iSEEindexResource-generics.html">precache()</a></code> function has for only
 job to remove the <code>localhost://</code> prefix from the URI, and
-cache the file located at the resulting file path using <em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>.</p>
+cache the file located at the resulting file path using <em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>.</p>
 </div>
 </div>
 <div class="section level3">
@@ -228,12 +228,12 @@ <h4 id="caching-2">Caching<a class="anchor" aria-label="anchor" href="#caching-2
 <p>The custom scheme <code>rcall</code> is entirely made up for the
 purpose described here; it is not in any way recognised as a standard
 scheme by the <a href="https://www.iana.org/assignments/uri-schemes/uri-schemes.xhtml" class="external-link">Internet
-Assigned Numbers Authority (IANA)</a>. As such, the <em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>
+Assigned Numbers Authority (IANA)</a>. As such, the <em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>
 package cannot possibly know how to handle that custom scheme.</p>
 <p>In this instance, the <code><a href="../reference/iSEEindexResource-generics.html">precache()</a></code> function has the job to
 remove the <code>rcall://</code> prefix from the URI, evaluate the
 remainder of the URI as R code, and cache the file located at the
-resulting file path using <em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>.</p>
+resulting file path using <em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>.</p>
 </div>
 </div>
 <div class="section level3">
@@ -255,23 +255,23 @@ <h4 id="structure-3">Structure<a class="anchor" aria-label="anchor" href="#struc
 <h4 id="caching-3">Caching<a class="anchor" aria-label="anchor" href="#caching-3"></a>
 </h4>
 <p>Now, while the scheme <code>s3</code> is recognised by the <a href="https://aws.amazon.com/cli/" class="external-link">AWS Command Line Interface</a>, the
-<em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>
+<em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>
 package does not know how to deal with it.</p>
 <p>In this instance, the <code><a href="../reference/iSEEindexResource-generics.html">precache()</a></code> function has the job to
 parse the URI for information that is passed to the <em><a href="https://CRAN.R-project.org/package=paws.storage" class="external-link">paws.storage</a></em>
-package to download the file, which is then cached using <em><a href="https://bioconductor.org/packages/3.17/BiocFileCache" class="external-link">BiocFileCache</a></em>.</p>
+package to download the file, which is then cached using <em><a href="https://bioconductor.org/packages/3.19/BiocFileCache" class="external-link">BiocFileCache</a></em>.</p>
 </div>
 </div>
 </div>
 <div class="section level2">
 <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" href="#reproducibility"></a>
 </h2>
-<p>The <em><a href="https://bioconductor.org/packages/3.17/iSEEindex" class="external-link">iSEEindex</a></em>
-package (Rue-Albrecht, 2022) was made possible thanks to:</p>
+<p>The <em><a href="https://bioconductor.org/packages/3.19/iSEEindex" class="external-link">iSEEindex</a></em>
+package (Rue-Albrecht and Marini, 2024) was made possible thanks to:</p>
 <ul>
-<li>R (R Core Team, 2023)</li>
+<li>R (R Core Team, 2024)</li>
 <li>
-<em><a href="https://bioconductor.org/packages/3.17/BiocStyle" class="external-link">BiocStyle</a></em>
+<em><a href="https://bioconductor.org/packages/3.19/BiocStyle" class="external-link">BiocStyle</a></em>
 (Oleś, 2023)</li>
 <li>
 <em><a href="https://CRAN.R-project.org/package=knitr" class="external-link">knitr</a></em> (Xie,
@@ -290,7 +290,7 @@ <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" hr
 <em><a href="https://CRAN.R-project.org/package=testthat" class="external-link">testthat</a></em>
 (Wickham, 2011)</li>
 </ul>
-<p>This package was developed using <em><a href="https://bioconductor.org/packages/3.17/biocthis" class="external-link">biocthis</a></em>.</p>
+<p>This package was developed using <em><a href="https://bioconductor.org/packages/3.19/biocthis" class="external-link">biocthis</a></em>.</p>
 <p>Code for creating the vignette</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co">## Create the vignette</span></span>
@@ -301,71 +301,70 @@ <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" hr
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://yihui.org/knitr/" class="external-link">"knitr"</a></span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/knit.html" class="external-link">knit</a></span><span class="op">(</span><span class="st">"resources.Rmd"</span>, tangle <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
 <p>Date the vignette was generated.</p>
-<pre><code><span><span class="co">#&gt; [1] "2023-07-06 20:02:07 UTC"</span></span></code></pre>
+<pre><code><span><span class="co">#&gt; [1] "2024-02-22 12:57:20 UTC"</span></span></code></pre>
 <p>Wallclock time spent generating the vignette.</p>
-<pre><code><span><span class="co">#&gt; Time difference of 0.627 secs</span></span></code></pre>
+<pre><code><span><span class="co">#&gt; Time difference of 0.528 secs</span></span></code></pre>
 <p><code>R</code> session information.</p>
 <pre><code><span><span class="co">#&gt; <span style="color: #00BBBB; font-weight: bold;">─ Session info ───────────────────────────────────────────────────────────────────────────────────</span></span></span>
 <span><span class="co">#&gt;  <span style="color: #555555; font-style: italic;">setting </span> <span style="color: #555555; font-style: italic;">value</span></span></span>
-<span><span class="co">#&gt;  version  R version 4.3.1 (2023-06-16)</span></span>
-<span><span class="co">#&gt;  os       Ubuntu 22.04.2 LTS</span></span>
+<span><span class="co">#&gt;  version  R Under development (unstable) (2024-02-19 r85946)</span></span>
+<span><span class="co">#&gt;  os       Ubuntu 22.04.3 LTS</span></span>
 <span><span class="co">#&gt;  system   x86_64, linux-gnu</span></span>
 <span><span class="co">#&gt;  ui       X11</span></span>
 <span><span class="co">#&gt;  language en</span></span>
 <span><span class="co">#&gt;  collate  en_US.UTF-8</span></span>
 <span><span class="co">#&gt;  ctype    en_US.UTF-8</span></span>
 <span><span class="co">#&gt;  tz       UTC</span></span>
-<span><span class="co">#&gt;  date     2023-07-06</span></span>
+<span><span class="co">#&gt;  date     2024-02-22</span></span>
 <span><span class="co">#&gt;  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB; font-weight: bold;">─ Packages ───────────────────────────────────────────────────────────────────────────────────────</span></span></span>
 <span><span class="co">#&gt;  <span style="color: #555555; font-style: italic;">package    </span> <span style="color: #555555; font-style: italic;">*</span> <span style="color: #555555; font-style: italic;">version</span> <span style="color: #555555; font-style: italic;">date (UTC)</span> <span style="color: #555555; font-style: italic;">lib</span> <span style="color: #555555; font-style: italic;">source</span></span></span>
-<span><span class="co">#&gt;  backports     1.4.1   <span style="color: #555555;">2021-12-13</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  bibtex        0.5.1   <span style="color: #555555;">2023-01-26</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  BiocManager   1.30.21 <span style="color: #555555;">2023-06-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  BiocStyle   * 2.28.0  <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
-<span><span class="co">#&gt;  bookdown      0.34    <span style="color: #555555;">2023-05-09</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  bslib         0.5.0   <span style="color: #555555;">2023-06-09</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  cachem        1.0.8   <span style="color: #555555;">2023-05-01</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  cli           3.6.1   <span style="color: #555555;">2023-03-23</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  desc          1.4.2   <span style="color: #555555;">2022-09-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  digest        0.6.32  <span style="color: #555555;">2023-06-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  evaluate      0.21    <span style="color: #555555;">2023-05-05</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  fastmap       1.1.1   <span style="color: #555555;">2023-02-24</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  fontawesome   0.5.1   <span style="color: #555555;">2023-04-18</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  fs            1.6.2   <span style="color: #555555;">2023-04-25</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  generics      0.1.3   <span style="color: #555555;">2022-07-05</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  glue          1.6.2   <span style="color: #555555;">2022-02-24</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  htmltools     0.5.5   <span style="color: #555555;">2023-03-23</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  jquerylib     0.1.4   <span style="color: #555555;">2021-04-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  jsonlite      1.8.7   <span style="color: #555555;">2023-06-29</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  lubridate     1.9.2   <span style="color: #555555;">2023-02-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  memoise       2.0.1   <span style="color: #555555;">2021-11-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  pkgdown       2.0.7   <span style="color: #555555;">2022-12-14</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  plyr          1.8.8   <span style="color: #555555;">2022-11-11</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  R6            2.5.1   <span style="color: #555555;">2021-08-19</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  Rcpp          1.0.11  <span style="color: #555555;">2023-07-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  RefManageR  * 1.4.0   <span style="color: #555555;">2022-09-30</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  rlang         1.1.1   <span style="color: #555555;">2023-04-28</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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-<span><span class="co">#&gt;  rprojroot     2.0.3   <span style="color: #555555;">2022-04-02</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  sass          0.4.6   <span style="color: #555555;">2023-05-03</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  sessioninfo * 1.2.2   <span style="color: #555555;">2021-12-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  stringi       1.7.12  <span style="color: #555555;">2023-01-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  stringr       1.5.0   <span style="color: #555555;">2022-12-02</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  systemfonts   1.0.4   <span style="color: #555555;">2022-02-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  textshaping   0.3.6   <span style="color: #555555;">2021-10-13</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  timechange    0.2.0   <span style="color: #555555;">2023-01-11</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  vctrs         0.6.3   <span style="color: #555555;">2023-06-14</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  xfun          0.39    <span style="color: #555555;">2023-04-20</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  xml2          1.3.5   <span style="color: #555555;">2023-07-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  yaml          2.3.7   <span style="color: #555555;">2023-01-23</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
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+<span><span class="co">#&gt;  bibtex        0.5.1   <span style="color: #555555;">2023-01-26</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  BiocManager   1.30.22 <span style="color: #555555;">2023-08-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  BiocStyle   * 2.31.0  <span style="color: #555555;">2023-10-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">Bioconductor</span></span></span>
+<span><span class="co">#&gt;  bookdown      0.37    <span style="color: #555555;">2023-12-01</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  bslib         0.6.1   <span style="color: #555555;">2023-11-28</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  cachem        1.0.8   <span style="color: #555555;">2023-05-01</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  cli           3.6.2   <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  desc          1.4.3   <span style="color: #555555;">2023-12-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  digest        0.6.34  <span style="color: #555555;">2024-01-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  evaluate      0.23    <span style="color: #555555;">2023-11-01</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  fastmap       1.1.1   <span style="color: #555555;">2023-02-24</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  fontawesome   0.5.2   <span style="color: #555555;">2023-08-19</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  fs            1.6.3   <span style="color: #555555;">2023-07-20</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  generics      0.1.3   <span style="color: #555555;">2022-07-05</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  glue          1.7.0   <span style="color: #555555;">2024-01-09</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  htmltools     0.5.7   <span style="color: #555555;">2023-11-03</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  httr          1.4.7   <span style="color: #555555;">2023-08-15</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  jquerylib     0.1.4   <span style="color: #555555;">2021-04-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  jsonlite      1.8.8   <span style="color: #555555;">2023-12-04</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  knitr         1.45    <span style="color: #555555;">2023-10-30</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  lifecycle     1.0.4   <span style="color: #555555;">2023-11-07</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  lubridate     1.9.3   <span style="color: #555555;">2023-09-27</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  magrittr      2.0.3   <span style="color: #555555;">2022-03-30</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  memoise       2.0.1   <span style="color: #555555;">2021-11-26</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  pkgdown       2.0.7   <span style="color: #555555;">2022-12-14</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  plyr          1.8.9   <span style="color: #555555;">2023-10-02</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  purrr         1.0.2   <span style="color: #555555;">2023-08-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  R6            2.5.1   <span style="color: #555555;">2021-08-19</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  ragg          1.2.7   <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  Rcpp          1.0.12  <span style="color: #555555;">2024-01-09</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  RefManageR  * 1.4.0   <span style="color: #555555;">2022-09-30</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  rlang         1.1.3   <span style="color: #555555;">2024-01-10</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  rmarkdown     2.25    <span style="color: #555555;">2023-09-18</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  sass          0.4.8   <span style="color: #555555;">2023-12-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  sessioninfo * 1.2.2   <span style="color: #555555;">2021-12-06</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  stringi       1.8.3   <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  stringr       1.5.1   <span style="color: #555555;">2023-11-14</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  systemfonts   1.0.5   <span style="color: #555555;">2023-10-09</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  textshaping   0.3.7   <span style="color: #555555;">2023-10-09</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  timechange    0.3.0   <span style="color: #555555;">2024-01-18</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  vctrs         0.6.5   <span style="color: #555555;">2023-12-01</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  xfun          0.42    <span style="color: #555555;">2024-02-08</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  xml2          1.3.6   <span style="color: #555555;">2023-12-04</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
+<span><span class="co">#&gt;  yaml          2.3.8   <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[2]</span> <span style="color: #555555;">CRAN (R 4.4.0)</span></span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; <span style="color: #555555;"> [1] /__w/_temp/Library</span></span></span>
 <span><span class="co">#&gt; <span style="color: #555555;"> [2] /usr/local/lib/R/site-library</span></span></span>
@@ -376,7 +375,7 @@ <h2 id="reproducibility">Reproducibility<a class="anchor" aria-label="anchor" hr
 <div class="section level2">
 <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#bibliography"></a>
 </h2>
-<p>This vignette was generated using <em><a href="https://bioconductor.org/packages/3.17/BiocStyle" class="external-link">BiocStyle</a></em>
+<p>This vignette was generated using <em><a href="https://bioconductor.org/packages/3.19/BiocStyle" class="external-link">BiocStyle</a></em>
 (Oleś, 2023) with <em><a href="https://CRAN.R-project.org/package=knitr" class="external-link">knitr</a></em> (Xie,
 2023) and <em><a href="https://CRAN.R-project.org/package=rmarkdown" class="external-link">rmarkdown</a></em>
 (Allaire, Xie, Dervieux et al., 2023) running behind the scenes.</p>
@@ -385,7 +384,7 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 <p>
 <a id="bib-allaire2023rmarkdown"></a><a href="#cite-allaire2023rmarkdown">[1]</a><cite>
 J. Allaire, Y. Xie, C. Dervieux, et al. <em>rmarkdown: Dynamic Documents
-for R</em>. R package version 2.23. 2023. URL:
+for R</em>. R package version 2.25. 2023. URL:
 <a href="https://github.com/rstudio/rmarkdown" class="external-link">https://github.com/rstudio/rmarkdown</a>.</cite>
 </p>
 <p>
@@ -398,23 +397,23 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 <p>
 <a id="bib-ole2023biocstyle"></a><a href="#cite-ole2023biocstyle">[3]</a><cite>
 A. Oleś. <em>BiocStyle: Standard styles for vignettes and other
-Bioconductor documents</em>. R package version 2.28.0. 2023. DOI:
+Bioconductor documents</em>. R package version 2.31.0. 2023. DOI:
 <a href="https://doi.org/10.18129/B9.bioc.BiocStyle" class="external-link">10.18129/B9.bioc.BiocStyle</a>.
 URL:
 <a href="https://bioconductor.org/packages/BiocStyle" class="external-link">https://bioconductor.org/packages/BiocStyle</a>.</cite>
 </p>
 <p>
-<a id="bib-2023language"></a><a href="#cite-2023language">[4]</a><cite>
+<a id="bib-2024language"></a><a href="#cite-2024language">[4]</a><cite>
 R Core Team. <em>R: A Language and Environment for Statistical
 Computing</em>. R Foundation for Statistical Computing. Vienna, Austria,
-2023. URL:
+2024. URL:
 <a href="https://www.R-project.org/" class="external-link">https://www.R-project.org/</a>.</cite>
 </p>
 <p>
-<a id="bib-ruealbrecht2022iseeindex"></a><a href="#cite-ruealbrecht2022iseeindex">[5]</a><cite>
-K. Rue-Albrecht. <em>iSEEindex: iSEE extension for a landing page to a
-custom collection of data sets</em>. R package version 0.99.13. 2022.
-URL:
+<a id="bib-ruealbrecht2024iseeindex"></a><a href="#cite-ruealbrecht2024iseeindex">[5]</a><cite>
+K. Rue-Albrecht and F. Marini. <em>iSEEindex: iSEE extension for a
+landing page to a custom collection of data sets</em>. R package version
+1.1.1. 2024. URL:
 <a href="https://github.com/iSEE/iSEEindex" class="external-link">https://github.com/iSEE/iSEEindex</a>.</cite>
 </p>
 <p>
@@ -432,7 +431,7 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 <p>
 <a id="bib-xie2023knitr"></a><a href="#cite-xie2023knitr">[8]</a><cite>
 Y. Xie. <em>knitr: A General-Purpose Package for Dynamic Report
-Generation in R</em>. R package version 1.43. 2023. URL:
+Generation in R</em>. R package version 1.45. 2023. URL:
 <a href="https://yihui.org/knitr/" class="external-link">https://yihui.org/knitr/</a>.</cite>
 </p>
 <!-- Links -->
@@ -451,7 +450,7 @@ <h2 id="bibliography">Bibliography<a class="anchor" aria-label="anchor" href="#b
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+<p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/authors.html b/authors.html
index 4f2d462..3d48737 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -72,6 +72,10 @@ <h1>Authors</h1>
           <p><strong>Thomas Sandmann</strong>. Contributor. <a href="https://orcid.org/0000-0002-6601-8890" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
         </li>
+        <li>
+          <p><strong>Federico Marini</strong>. Author. <a href="https://orcid.org/0000-0003-3252-7758" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
+          </p>
+        </li>
         <li>
           <p><strong>Denali Therapeutics</strong>. Funder. 
           </p>
@@ -85,15 +89,15 @@ <h1 id="citation">Citation</h1>
     </div>
 
 
-    <p>Rue-Albrecht K (2023).
+    <p>Rue-Albrecht K, Marini F (2024).
 <em>iSEEindex: iSEE extension for a landing page to a custom collection of data sets</em>.
-R package version 0.99.13, <a href="https://github.com/iSEE/iSEEindex" class="external-link">https://github.com/iSEE/iSEEindex</a>. 
+R package version 1.1.1, <a href="https://github.com/iSEE/iSEEindex" class="external-link">https://github.com/iSEE/iSEEindex</a>. 
 </p>
     <pre>@Manual{,
   title = {iSEEindex: iSEE extension for a landing page to a custom collection of data sets},
-  author = {Kevin Rue-Albrecht},
-  year = {2023},
-  note = {R package version 0.99.13},
+  author = {Kevin Rue-Albrecht and Federico Marini},
+  year = {2024},
+  note = {R package version 1.1.1},
   url = {https://github.com/iSEE/iSEEindex},
 }</pre>
 
@@ -104,7 +108,7 @@ <h1 id="citation">Citation</h1>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/index.html b/index.html
index 1b9c996..d8243ac 100644
--- a/index.html
+++ b/index.html
@@ -38,7 +38,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -235,6 +235,7 @@ <h2 data-toc-skip>Citation</h2>
 <h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
 <li>Kevin Rue-Albrecht <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-3899-3872" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li>Federico Marini <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0003-3252-7758" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
 <li>Denali Therapeutics <br><small class="roles"> Funder </small>  </li>
 <li><a href="authors.html">More about authors...</a></li>
 </ul>
@@ -257,7 +258,7 @@ <h2 data-toc-skip>Dev status</h2>
 
       <footer><div class="copyright">
   <p></p>
-<p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+<p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/news/index.html b/news/index.html
index f23848b..7c282a5 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -63,6 +63,10 @@ <h1 data-toc-skip>Changelog <small></small></h1>
       <small>Source: <a href="https://github.com/iSEE/iSEEindex/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="1.1.1" id="iseeindex-111">iSEEindex 1.1.1<a class="anchor" aria-label="anchor" href="#iseeindex-111"></a></h2>
+<ul><li>Add possibility to customise the title of the app.</li>
+</ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.99.13" id="iseeindex-09913">iSEEindex 0.99.13<a class="anchor" aria-label="anchor" href="#iseeindex-09913"></a></h2>
 <ul><li>Added possibility to inject custom header and footer in landing page.</li>
@@ -130,7 +134,7 @@ <h2 class="page-header" data-toc-text="0.99.0" id="iseeindex-0990">iSEEindex 0.9
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/pkgdown.yml b/pkgdown.yml
index 7b8d526..798a584 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   header: header.html
   iSEEindex: iSEEindex.html
   resources: resources.html
-last_built: 2023-07-06T20:01Z
+last_built: 2024-02-22T12:56Z
 
diff --git a/reference/iSEEindex-pkg.html b/reference/iSEEindex-pkg.html
index 13d458a..88f3b76 100644
--- a/reference/iSEEindex-pkg.html
+++ b/reference/iSEEindex-pkg.html
@@ -21,7 +21,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -92,7 +92,7 @@ <h2>See also</h2>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/reference/iSEEindex.html b/reference/iSEEindex.html
index 842c37f..4bc2108 100644
--- a/reference/iSEEindex.html
+++ b/reference/iSEEindex.html
@@ -19,7 +19,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -249,7 +249,7 @@ <h2>Examples</h2>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/reference/iSEEindexHttpsResource-class.html b/reference/iSEEindexHttpsResource-class.html
index 5284f53..93159b7 100644
--- a/reference/iSEEindexHttpsResource-class.html
+++ b/reference/iSEEindexHttpsResource-class.html
@@ -19,7 +19,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -130,7 +130,7 @@ <h2>Examples</h2>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/reference/iSEEindexLocalhostResource-class.html b/reference/iSEEindexLocalhostResource-class.html
index 3369dc7..a8c5774 100644
--- a/reference/iSEEindexLocalhostResource-class.html
+++ b/reference/iSEEindexLocalhostResource-class.html
@@ -19,7 +19,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -146,7 +146,7 @@ <h2>Examples</h2>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/reference/iSEEindexRcallResource-class.html b/reference/iSEEindexRcallResource-class.html
index 486bbcd..9cb6ea3 100644
--- a/reference/iSEEindexRcallResource-class.html
+++ b/reference/iSEEindexRcallResource-class.html
@@ -19,7 +19,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -144,7 +144,7 @@ <h2>Examples</h2>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/reference/iSEEindexResource-class.html b/reference/iSEEindexResource-class.html
index 347ed74..a38ead9 100644
--- a/reference/iSEEindexResource-class.html
+++ b/reference/iSEEindexResource-class.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -148,7 +148,7 @@ <h2>Examples</h2>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/reference/iSEEindexResource-generics.html b/reference/iSEEindexResource-generics.html
index 534865d..4862ba4 100644
--- a/reference/iSEEindexResource-generics.html
+++ b/reference/iSEEindexResource-generics.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -116,8 +116,8 @@ <h2>Examples</h2>
 <span class="r-in"><span>  uri <span class="op">=</span> <span class="st">"rcall://system.file(package='iSEEindex','ReprocessedAllenData_config_01.R')"</span></span></span>
 <span class="r-in"><span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">precache</span><span class="op">(</span><span class="va">x</span>, <span class="va">bfc</span>, <span class="st">"ID0"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>                                                           BFC1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> "/tmp/Rtmp0z7NiQ/c2626c09d44_ReprocessedAllenData_config_01.R" </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>                                                            BFC1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> "/tmp/RtmptNSUps/18814398f88d_ReprocessedAllenData_config_01.R" </span>
 </code></pre></div>
     </div>
   </div>
@@ -128,7 +128,7 @@ <h2>Examples</h2>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/reference/iSEEindexS3Resource-class.html b/reference/iSEEindexS3Resource-class.html
index 1d9d506..485abee 100644
--- a/reference/iSEEindexS3Resource-class.html
+++ b/reference/iSEEindexS3Resource-class.html
@@ -21,7 +21,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -204,7 +204,7 @@ <h2>Examples</h2>
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">
diff --git a/reference/index.html b/reference/index.html
index 1873680..8f4573e 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">iSEEindex</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.13</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.1.1</span>
       </span>
     </div>
 
@@ -103,7 +103,7 @@ <h2 id="all-functions">All functions <a href="#all-functions" class="anchor" ari
 
 
       <footer><div class="copyright">
-  <p></p><p>Developed by Kevin Rue-Albrecht, Denali Therapeutics.</p>
+  <p></p><p>Developed by Kevin Rue-Albrecht, Federico Marini, Denali Therapeutics.</p>
 </div>
 
 <div class="pkgdown">