Updated contents at 20240308-063354

NBISweden · Mar 8, 2024 · e552a71 · e552a71
1 parent 76cbcb1
commit e552a71
Show file tree

Hide file tree

Showing 304 changed files with 1,067,912 additions and 204 deletions.
diff --git a/2403-canvas/home_schedule.html b/2403-canvas/home_schedule.html
@@ -371,7 +371,7 @@
 Johan Reimegård
 </td>
 </tr>
-<tr grouplength="7">
+<tr groupLength="7">
 <td colspan="3" style="background:white;">
 <strong>
 <p style="font-size:110%;padding-top:10px;padding-bottom:5px;margin-top:10px;">
@@ -454,182 +454,6 @@
 Nima Rafati
 </td>
 </tr>
-<tr grouplength="8">
-<td colspan="3" style="background:white;">
-<strong>
-<p style="font-size:110%;padding-top:10px;padding-bottom:5px;margin-top:10px;">
-<span style="font-weight:bold;"><span style="color:#95b540;"><i class="fas fa-calendar" style="margin-left:5px;margin-right:5px;"></i></span>14-Mar-2024</span><span style="color:white;border-radius:4px;padding-right:4px;padding-left:4px;background:#95b540;margin-left:9px;margin-right:7px;">Thu</span><span style="color:#95b540;"><i class="fas fa-map-marker-alt" style="margin-left:5px;margin-right:5px;"></i></span>Experimental classroom (10:203)
-</p>
-</strong>
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-09:00 - 10:00
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="margin-right:5px;">DGE</span>
-</td>
-<td style="text-align:left;">
-Julie Lorent
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-10:00 - 10:30
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="color:white;font-weight:bold;border-radius:4px;padding:4px;background:#BDBDBD;">Coffee Break</span>
-</td>
-<td style="text-align:left;">
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-10:30 - 12:00
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="margin-right:5px;">DGE advanced</span>
-</td>
-<td style="text-align:left;">
-Julie Lorent
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-12:00 - 13:00
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="color:white;font-weight:bold;border-radius:4px;padding:4px;background:#BDBDBD;">Lunch</span>
-</td>
-<td style="text-align:left;">
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-13:00 - 14:00
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="margin-right:5px;">GSA &amp; GSEA</span>
-</td>
-<td style="text-align:left;">
-Nima Rafati
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-14:00 - 14:30
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="color:white;font-weight:bold;border-radius:4px;padding:4px;background:#BDBDBD;">Coffee Break</span>
-</td>
-<td style="text-align:left;">
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-14:30 - 15:30
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="margin-right:5px;">GSA &amp; GSEA</span>
-</td>
-<td style="text-align:left;">
-Nima Rafati
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-15:30 - 16:00
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="margin-right:5px;">Online Repositories</span>
-</td>
-<td style="text-align:left;">
-Johan Reimegård
-</td>
-</tr>
-<tr groupLength="7">
-<td colspan="3" style="background:white;">
-<strong>
-<p style="font-size:110%;padding-top:10px;padding-bottom:5px;margin-top:10px;">
-<span style="font-weight:bold;"><span style="color:#95b540;"><i class="fas fa-calendar" style="margin-left:5px;margin-right:5px;"></i></span>15-Mar-2024</span><span style="color:white;border-radius:4px;padding-right:4px;padding-left:4px;background:#95b540;margin-left:9px;margin-right:7px;">Fri</span><span style="color:#95b540;"><i class="fas fa-map-marker-alt" style="margin-left:5px;margin-right:5px;"></i></span>Experimental classroom (10:203)
-</p>
-</strong>
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-09:00 - 10:00
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="margin-right:5px;">Reading Bioinformatics</span>
-</td>
-<td style="text-align:left;">
-Johan Reimegård
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-10:00 - 10:30
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="color:white;font-weight:bold;border-radius:4px;padding:4px;background:#BDBDBD;">Coffee Break</span>
-</td>
-<td style="text-align:left;">
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-10:30 - 12:00
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="margin-right:5px;">Pseudoaligners</span>
-</td>
-<td style="text-align:left;">
-Johan Reimegård
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-12:00 - 13:30
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="color:white;font-weight:bold;border-radius:4px;padding:4px;background:#BDBDBD;">Lunch</span>
-</td>
-<td style="text-align:left;">
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-13:30 - 14:00
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="margin-right:5px;">Free Exercises</span>
-</td>
-<td style="text-align:left;">
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-14:00 - 14:30
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="color:white;font-weight:bold;border-radius:4px;padding:4px;background:#BDBDBD;">Coffee Break</span>
-</td>
-<td style="text-align:left;">
-</td>
-</tr>
-<tr>
-<td style="text-align:left;width: 7em; ">
-14:30 - 15:00
-</td>
-<td style="text-align:left;width: 16em; ">
-<span style="margin-right:5px;">Conclusion</span>
-</td>
-<td style="text-align:left;">
-Johan Reimegård
-</td>
-</tr>
 </tbody>
 </table>
 <!-- marker legend -->

diff --git a/2403-canvas/index.html b/2403-canvas/index.html
@@ -201,7 +201,7 @@ <h1>Analysis of RNA-Seq Data</h1>
 <hr />
 <div class="landing-update">
 <p class="small" style="color:#bdbdbd;">
-Last updated on <svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#bdbdbd;overflow:visible;position:relative;"><path d="M152 24c0-13.3-10.7-24-24-24s-24 10.7-24 24V64H64C28.7 64 0 92.7 0 128v16 48V448c0 35.3 28.7 64 64 64H384c35.3 0 64-28.7 64-64V192 144 128c0-35.3-28.7-64-64-64H344V24c0-13.3-10.7-24-24-24s-24 10.7-24 24V64H152V24zM48 192h80v56H48V192zm0 104h80v64H48V296zm128 0h96v64H176V296zm144 0h80v64H320V296zm80-48H320V192h80v56zm0 160v40c0 8.8-7.2 16-16 16H320V408h80zm-128 0v56H176V408h96zm-144 0v56H64c-8.8 0-16-7.2-16-16V408h80zM272 248H176V192h96v56z"/></svg> 07-Mar-2024 at <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:#bdbdbd;overflow:visible;position:relative;"><path d="M464 256A208 208 0 1 1 48 256a208 208 0 1 1 416 0zM0 256a256 256 0 1 0 512 0A256 256 0 1 0 0 256zM232 120V256c0 8 4 15.5 10.7 20l96 64c11 7.4 25.9 4.4 33.3-6.7s4.4-25.9-6.7-33.3L280 243.2V120c0-13.3-10.7-24-24-24s-24 10.7-24 24z"/></svg> 09:21:21 PM .
+Last updated on <svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#bdbdbd;overflow:visible;position:relative;"><path d="M152 24c0-13.3-10.7-24-24-24s-24 10.7-24 24V64H64C28.7 64 0 92.7 0 128v16 48V448c0 35.3 28.7 64 64 64H384c35.3 0 64-28.7 64-64V192 144 128c0-35.3-28.7-64-64-64H344V24c0-13.3-10.7-24-24-24s-24 10.7-24 24V64H152V24zM48 192h80v56H48V192zm0 104h80v64H48V296zm128 0h96v64H176V296zm144 0h80v64H320V296zm80-48H320V192h80v56zm0 160v40c0 8.8-7.2 16-16 16H320V408h80zm-128 0v56H176V408h96zm-144 0v56H64c-8.8 0-16-7.2-16-16V408h80zM272 248H176V192h96v56z"/></svg> 08-Mar-2024 at <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:#bdbdbd;overflow:visible;position:relative;"><path d="M464 256A208 208 0 1 1 48 256a208 208 0 1 1 416 0zM0 256a256 256 0 1 0 512 0A256 256 0 1 0 0 256zM232 120V256c0 8 4 15.5 10.7 20l96 64c11 7.4 25.9 4.4 33.3-6.7s4.4-25.9-6.7-33.3L280 243.2V120c0-13.3-10.7-24-24-24s-24 10.7-24 24z"/></svg> 05:31:47 AM .
 </p>
 </div>
 </div>

diff --git a/2403-canvas/lab_dge_files/figure-html/unnamed-chunk-27-1.png b/2403-canvas/lab_dge_files/figure-html/unnamed-chunk-27-1.png
diff --git a/2403-canvas/lab_dge_files/figure-html/unnamed-chunk-27-2.png b/2403-canvas/lab_dge_files/figure-html/unnamed-chunk-27-2.png
diff --git a/2403-canvas/lab_eda_files/figure-html/unnamed-chunk-18-1.png b/2403-canvas/lab_eda_files/figure-html/unnamed-chunk-18-1.png
diff --git a/2403-canvas/lab_functional_files/figure-html/unnamed-chunk-11-1.png b/2403-canvas/lab_functional_files/figure-html/unnamed-chunk-11-1.png
diff --git a/2403-canvas/lab_functional_files/figure-html/unnamed-chunk-12-1.png b/2403-canvas/lab_functional_files/figure-html/unnamed-chunk-12-1.png
diff --git a/2403-canvas/lab_r.html b/2403-canvas/lab_r.html
@@ -405,20 +405,20 @@ <h1><span class="header-section-number">6</span> Functions</h1>
 
 # sort
 sort(x)</code></pre>
-<pre><code>##  [1]  17 184 105 149  82  52 195  39  15  65
+<pre><code>##  [1]  29 160 183  26  78 162 194  67 196 185
 ## [1] 10
-## [1] 903
-## [1] 90.3
-## [1] 73.5
-## [1] 15
-##  [1] 2.833213 5.214936 4.653960 5.003946 4.406719 3.951244 5.273000 3.663562
-##  [9] 2.708050 4.174387
-##  [1] 2.415495e+07 8.131762e+79 3.989520e+45 5.127171e+64 4.093997e+35
-##  [6] 3.831008e+22 4.868823e+84 8.659340e+16 3.269017e+06 1.694889e+28
-##  [1]  4.123106 13.564660 10.246951 12.206556  9.055385  7.211103 13.964240
-##  [8]  6.244998  3.872983  8.062258
-##  [1]  17 184 105 149  82  52 195  39  15  65
-##  [1]  15  17  39  52  65  82 105 149 184 195</code></pre>
+## [1] 1280
+## [1] 128
+## [1] 161
+## [1] 26
+##  [1] 3.367296 5.075174 5.209486 3.258097 4.356709 5.087596 5.267858 4.204693
+##  [9] 5.278115 5.220356
+##  [1] 3.931334e+12 3.069850e+69 2.991508e+79 1.957296e+11 7.498417e+33
+##  [6] 2.268329e+70 1.791140e+84 1.252363e+29 1.323483e+85 2.210442e+80
+##  [1]  5.385165 12.649111 13.527749  5.099020  8.831761 12.727922 13.928388
+##  [8]  8.185353 14.000000 13.601471
+##  [1]  29 160 183  26  78 162 194  67 196 185
+##  [1]  26  29  67  78 160 162 183 185 194 196</code></pre>
 <p>Some useful string functions.</p>
 <pre class="r"><code>a &lt;- &quot;sunny&quot;
 b &lt;- &quot;day&quot;

diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-24-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-24-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-25-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-25-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-26-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-26-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-28-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-28-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-29-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-29-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-30-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-30-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-31-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-31-1.png
diff --git a/2403-canvas/slide_clustering.html b/2403-canvas/slide_clustering.html
@@ -133,13 +133,15 @@
 -   Dependent on number of K (clusters) new centroids are created
 
 &lt;!-- &lt;div style="text-align: center;"&gt; --&gt;
-&lt;!-- &lt;img src="data/kmeans.gif" alt="Alt text for the GIF" style="width: 65%; height: auto;"&gt; --&gt;
+&lt;!-- &lt;img src="data/kmeans_3.gif" alt="Alt text for the GIF" style="width: 65%; height: auto;"&gt; --&gt;
 &lt;!-- &lt;/div&gt; --&gt;
-![](data/kmeans_DS.gif)
+---
+name: Centroid-based2
+![](data/Kmeans_3_DS.gif){width=50%}
 
 
 ---
-name: Centroid-based2
+name: Centroid-based3
 ## Centroid-based: K-means clustering
 -   One of the most commonly used clustering methods
 
@@ -148,15 +150,12 @@
 -   Each data point is assigned to a cluster based on Euclidean distance from centroid.
 
 -   Dependent on number of K (clusters) new centroids are created
-
-&lt;!-- &lt;div style="text-align: center;"&gt; --&gt;
-&lt;!-- &lt;img src="data/kmeans_3.gif" alt="Alt text for the GIF" style="width: 65%; height: auto;"&gt; --&gt;
-&lt;!-- &lt;/div&gt; --&gt;
-![](data/Kmeans_3_DS.gif)
+---
+name: Centroid-based4
+![](data/kmeans_DS.gif){width=50%}
 
 
 ---
-
 name: optimal k
 ## What is optimal K?
 

diff --git a/2403-canvas/slide_clustering.pdf b/2403-canvas/slide_clustering.pdf
diff --git a/2403-canvas/slide_clustering_paulo.pdf b/2403-canvas/slide_clustering_paulo.pdf
diff --git a/2403-canvas/slide_dge.html b/2403-canvas/slide_dge.html
@@ -3,7 +3,7 @@
   <head>
     <title>Differential Gene Expression</title>
     <meta charset="utf-8" />
-    <meta name="author" content="Julie Lorent | 07-Mar-2024" />
+    <meta name="author" content="Julie Lorent | 08-Mar-2024" />
     <meta name="keywords" content="bioinformatics, course, scilifelab, nbis" />
     <script src="site_libs/header-attrs-2.21/header-attrs.js"></script>
     <link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
@@ -22,7 +22,7 @@
 ## Workshop on RNA-Seq
 ]
 .author[
-### <b>Julie Lorent</b> | 07-Mar-2024
+### <b>Julie Lorent</b> | 08-Mar-2024
 ]
 .institute[
 ### NBIS, SciLifeLab
@@ -294,7 +294,7 @@
 .end-text[
 &lt;p class="smaller"&gt;
 &lt;span class="small" style="line-height: 1.2;"&gt;Graphics from &lt;/span&gt;&lt;img src="./assets/freepik.jpg" style="max-height:20px; vertical-align:middle;"&gt;&lt;br&gt;
-Created: 07-Mar-2024 • &lt;a href="https://www.scilifelab.se/"&gt;SciLifeLab&lt;/a&gt; • &lt;a href="https://nbis.se/"&gt;NBIS&lt;/a&gt; 
+Created: 08-Mar-2024 • &lt;a href="https://www.scilifelab.se/"&gt;SciLifeLab&lt;/a&gt; • &lt;a href="https://nbis.se/"&gt;NBIS&lt;/a&gt; 
 &lt;/p&gt;
 ]
 

diff --git a/2403-canvas/slide_dge.pdf b/2403-canvas/slide_dge.pdf
diff --git a/2403-canvas/slide_functional.pdf b/2403-canvas/slide_functional.pdf
diff --git a/2403-canvas/slide_functional_paulo.pdf b/2403-canvas/slide_functional_paulo.pdf
diff --git a/2403-canvas/slide_preprocessing.html b/2403-canvas/slide_preprocessing.html
@@ -394,7 +394,7 @@
 .end-text[
 &lt;p class="smaller"&gt;
 &lt;span class="small" style="line-height: 1.2;"&gt;Graphics from &lt;/span&gt;&lt;img src="./assets/freepik.jpg" style="max-height:20px; vertical-align:middle;"&gt;&lt;br&gt;
-Created: 07-Mar-2024 • &lt;a href="https://www.scilifelab.se/"&gt;SciLifeLab&lt;/a&gt; • &lt;a href="https://nbis.se/"&gt;NBIS&lt;/a&gt; 
+Created: 08-Mar-2024 • &lt;a href="https://www.scilifelab.se/"&gt;SciLifeLab&lt;/a&gt; • &lt;a href="https://nbis.se/"&gt;NBIS&lt;/a&gt; 
 &lt;/p&gt;
 ]
 

diff --git a/2403-canvas/slide_preprocessing.pdf b/2403-canvas/slide_preprocessing.pdf
diff --git a/2403/Bad_RNASeq_Examples/Bias_GC_Content.jpeg b/2403/Bad_RNASeq_Examples/Bias_GC_Content.jpeg
diff --git a/2403/Bad_RNASeq_Examples/PBAT-base-composition.png b/2403/Bad_RNASeq_Examples/PBAT-base-composition.png
diff --git a/2403/Bad_RNASeq_Examples/Positional sequence bias in random primed libraries.png b/2403/Bad_RNASeq_Examples/Positional sequence bias in random primed libraries.png
diff --git a/2403/Bad_RNASeq_Examples/Technical_Duplication.png b/2403/Bad_RNASeq_Examples/Technical_Duplication.png
diff --git a/2403/Bad_RNASeq_Examples/biased_composition.png b/2403/Bad_RNASeq_Examples/biased_composition.png
diff --git a/2403/Bad_RNASeq_Examples/fastqc_sequence_length_distribution_plot-2-1.png b/2403/Bad_RNASeq_Examples/fastqc_sequence_length_distribution_plot-2-1.png
diff --git a/2403/Bad_RNASeq_Examples/rseqc_inner_distance_plot-1.png b/2403/Bad_RNASeq_Examples/rseqc_inner_distance_plot-1.png
diff --git a/2403/Dockerfile b/2403/Dockerfile
@@ -0,0 +1,42 @@
+# DOCKER FILE FOR WORKSHOP-RNASEQ
+# 2023 Roy Francis
+
+FROM rocker/verse:4.2.3
+LABEL Description="Docker image for NBIS workshop-rnaseq"
+LABEL Maintainer="roy.francis@nbis.se"
+LABEL org.opencontainers.image.source="https://github.com/NBISweden/workshop-rnaseq"
+
+RUN apt-get update -y \
+  && apt-get install --no-install-recommends -y \
+  libxml2-dev \
+  libssl-dev \
+  libcurl4-openssl-dev \
+  libudunits2-dev \
+  libopenblas-base \
+  libgdal-dev \
+  && wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb \
+  && apt-get install -y ./google-chrome-stable_current_amd64.deb \
+  && rm -rf google-chrome-stable_current_amd64.deb \
+  && rm -rf /var/lib/apt/lists/* \
+  && Rscript -e 'install.packages(c("bookdown","knitr","remotes","fontawesome","formattable","kableExtra","leaflet","pagedown","lubridate","markdown","xaringan","yaml"),repos = "https://packagemanager.posit.co/cran/__linux__/jammy/latest");' \
+  && mkdir /rmd
+
+RUN Rscript -e 'install.packages(c("BiocManager","dplyr","enrichR","ggplot2","gridExtra","pheatmap","pvclust","rafalib","stringr","tidyr","locfit"),repos = "https://packagemanager.posit.co/cran/__linux__/jammy/latest");'
+RUN Rscript -e 'BiocManager::install(c("DESeq2","edgeR","fgsea","biomaRt","GEOquery"));'
+WORKDIR /rmd
+CMD Rscript -e "rmarkdown::render_site()"
+
+# build container
+# docker build -t ghcr.io/nbisweden/workshop-rnaseq:1.0.0 .
+# docker tag ghcr.io/nbisweden/workshop-rnaseq:1.0.0 ghcr.io/nbisweden/workshop-rnaseq:latest
+
+# push to ghcr
+# docker login ghcr.io
+# docker push ghcr.io/nbisweden/workshop-rnaseq:1.0.0
+# docker push ghcr.io/nbisweden/workshop-rnaseq:latest
+
+# run container
+# render all files
+# docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-rnaseq:latest
+# render one file
+# docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-rnaseq:latest Rscript -e 'rmarkdown::render("index.Rmd")'
diff --git a/2403/assets/cover.png b/2403/assets/cover.png
diff --git a/2403/assets/end.png b/2403/assets/end.png
diff --git a/2403/assets/favicon.ico b/2403/assets/favicon.ico
diff --git a/2403/assets/favicon.png b/2403/assets/favicon.png
diff --git a/2403/assets/footer-lab.Rmd b/2403/assets/footer-lab.Rmd
@@ -0,0 +1,35 @@
+---
+title: "&nbsp;"
+---
+
+<footer class="footer">
+<div class="container footer-container">
+<div class="row">
+
+<hr>
+
+<div class="col-sm-8" style="text-align:left;vertical-align:middle;">
+<p class="small" style="color:#bdbdbd;">
+[NBIS](https://nbis.se/) • [SciLifeLab](https://www.scilifelab.se/)
+</p>
+</div>
+
+<div class="col-sm-4" style="text-align:right;vertical-align:middle;">
+<p style="color:#bdbdbd;">
+<span>
+<span class="footericon" style="padding-right:4px; padding-left:4px">
+<a href="https://nbis.se/">`r fontawesome::fa("globe-americas",fill="#bdbdbd")`</a>
+</span>
+<span class="footericon" style="padding-right:4px; padding-left:4px">
+<a href="https://twitter.com/NBISwe">`r fontawesome::fa("twitter",fill="#bdbdbd")`</a>
+</span>
+<span class="footericon" style="padding-left:4px">
+<a href="https://www.linkedin.com/company/nbisweden/">`r fontawesome::fa("linkedin",fill="#bdbdbd")`</a>
+</span>
+</span>
+</p>
+</div>
+
+</div>
+</div>
+</footer>