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+fd0f41ed

index.html

@@ -249,7 +249,7 @@ <h1 class="title">Glittr stats</h1>
 <span><span class="va">cat_table</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sort.html">sort</a></span><span class="op">(</span><span class="va">cat_table</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 </div>
-<p>Number of repositories: 613</p>
+<p>Number of repositories: 625</p>
 </section><section id="get-contributors-info" class="level2"><h2 class="anchored" data-anchor-id="get-contributors-info">Get contributors info</h2>
 <p>Using the GitHub REST API to get the number of contributors for each repository on glittr.org. This takes a few minutes, so if the contributors haven’t changed, it will use a cached version.</p>
 <div class="cell">
@@ -379,8 +379,8 @@ <h1 class="title">Glittr stats</h1>
 </details>
 </div>
 <ul>
-<li>Number of authors: 296</li>
-<li>Number of countries: 25</li>
+<li>Number of authors: 303</li>
+<li>Number of countries: 26</li>
 </ul></section><section id="parse-tag-data" class="level2"><h2 class="anchored" data-anchor-id="parse-tag-data">Parse tag data</h2>
 <p>Here, we create <code>tag_df</code> that contains information for each tag by using the glittr.org API.</p>
 <div class="cell">
@@ -443,27 +443,27 @@ <h1 class="title">Glittr stats</h1>
 <tbody>
 <tr class="odd">
 <td style="text-align: left;">Scripting and languages</td>
-<td style="text-align: right;">342</td>
+<td style="text-align: right;">343</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">Computational methods and pipelines</td>
-<td style="text-align: right;">58</td>
+<td style="text-align: right;">61</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">Omics analysis</td>
-<td style="text-align: right;">93</td>
+<td style="text-align: right;">99</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">Reproducibility and data management</td>
-<td style="text-align: right;">53</td>
+<td style="text-align: right;">54</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">Statistics and machine learning</td>
 <td style="text-align: right;">40</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">Others</td>
-<td style="text-align: right;">25</td>
+<td style="text-align: right;">26</td>
 </tr>
 </tbody>
 </table>
@@ -512,9 +512,9 @@ <h1 class="title">Glittr stats</h1>
 <span><span class="va">param3</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html">sum</a></span><span class="op">(</span><span class="va">nna_contr</span> <span class="op">&lt;=</span> <span class="fl">5</span><span class="op">)</span><span class="op">/</span><span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span><span class="op">(</span><span class="va">nna_contr</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <ul>
-<li>More than 10 contributors: 26.4%</li>
-<li>More than 1 contributor: 79.7%</li>
-<li>Between 1 and 5 contributors: 59.9%</li>
+<li>More than 10 contributors: 26%</li>
+<li>More than 1 contributor: 80.1%</li>
+<li>Between 1 and 5 contributors: 59.6%</li>
 </ul></section><section id="number-of-repositories-per-tag" class="level2"><h2 class="anchored" data-anchor-id="number-of-repositories-per-tag">Number of repositories per tag</h2>
 <p>This is figure 2C in the manuscript.</p>
 <div class="cell">
@@ -573,7 +573,7 @@ <h1 class="title">Glittr stats</h1>
 <tr class="odd">
 <td style="text-align: left;">R</td>
 <td style="text-align: left;">Scripting and languages</td>
-<td style="text-align: right;">248</td>
+<td style="text-align: right;">250</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">Python</td>
@@ -583,22 +583,22 @@ <h1 class="title">Glittr stats</h1>
 <tr class="odd">
 <td style="text-align: left;">Transcriptomics</td>
 <td style="text-align: left;">Omics analysis</td>
-<td style="text-align: right;">77</td>
+<td style="text-align: right;">83</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">RNA-seq</td>
 <td style="text-align: left;">Omics analysis</td>
-<td style="text-align: right;">73</td>
+<td style="text-align: right;">79</td>
 </tr>
 <tr class="odd">
-<td style="text-align: left;">Statistics</td>
-<td style="text-align: left;">Statistics and machine learning</td>
+<td style="text-align: left;">Next generation sequencing</td>
+<td style="text-align: left;">Omics analysis</td>
 <td style="text-align: right;">60</td>
 </tr>
 <tr class="even">
-<td style="text-align: left;">Next generation sequencing</td>
-<td style="text-align: left;">Omics analysis</td>
-<td style="text-align: right;">57</td>
+<td style="text-align: left;">Statistics</td>
+<td style="text-align: left;">Statistics and machine learning</td>
+<td style="text-align: right;">60</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">Data science</td>
@@ -611,24 +611,24 @@ <h1 class="title">Glittr stats</h1>
 <td style="text-align: right;">49</td>
 </tr>
 <tr class="odd">
+<td style="text-align: left;">Single-cell sequencing</td>
+<td style="text-align: left;">Omics analysis</td>
+<td style="text-align: right;">46</td>
+</tr>
+<tr class="even">
 <td style="text-align: left;">Machine learning</td>
 <td style="text-align: left;">Statistics and machine learning</td>
 <td style="text-align: right;">46</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;">Unix/Linux</td>
 <td style="text-align: left;">Scripting and languages</td>
-<td style="text-align: right;">39</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">Single-cell sequencing</td>
-<td style="text-align: left;">Omics analysis</td>
-<td style="text-align: right;">39</td>
+<td style="text-align: right;">40</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">Data management</td>
 <td style="text-align: left;">Reproducibility and data management</td>
-<td style="text-align: right;">35</td>
+<td style="text-align: right;">36</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">Reproducibility</td>
@@ -643,12 +643,12 @@ <h1 class="title">Glittr stats</h1>
 <tr class="odd">
 <td style="text-align: left;">General</td>
 <td style="text-align: left;">Others</td>
-<td style="text-align: right;">30</td>
+<td style="text-align: right;">31</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">FAIR data</td>
 <td style="text-align: left;">Reproducibility and data management</td>
-<td style="text-align: right;">29</td>
+<td style="text-align: right;">30</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">Variant analysis</td>
@@ -681,13 +681,13 @@ <h1 class="title">Glittr stats</h1>
 <td style="text-align: right;">17</td>
 </tr>
 <tr class="odd">
-<td style="text-align: left;">Docker</td>
-<td style="text-align: left;">Computational methods and pipelines</td>
-<td style="text-align: right;">14</td>
-</tr>
-<tr class="even">
 <td style="text-align: left;">ChIP-seq</td>
 <td style="text-align: left;">Omics analysis</td>
+<td style="text-align: right;">15</td>
+</tr>
+<tr class="even">
+<td style="text-align: left;">Docker</td>
+<td style="text-align: left;">Computational methods and pipelines</td>
 <td style="text-align: right;">14</td>
 </tr>
 <tr class="odd">
@@ -700,6 +700,21 @@ <h1 class="title">Glittr stats</h1>
 <td style="text-align: left;">Computational methods and pipelines</td>
 <td style="text-align: right;">12</td>
 </tr>
+<tr class="odd">
+<td style="text-align: left;">Image analysis</td>
+<td style="text-align: left;">Computational methods and pipelines</td>
+<td style="text-align: right;">11</td>
+</tr>
+<tr class="even">
+<td style="text-align: left;">ATAC-seq</td>
+<td style="text-align: left;">Omics analysis</td>
+<td style="text-align: right;">11</td>
+</tr>
+<tr class="odd">
+<td style="text-align: left;">Epigenetics</td>
+<td style="text-align: left;">Omics analysis</td>
+<td style="text-align: right;">11</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -778,7 +793,7 @@ <h1 class="title">Glittr stats</h1>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">NBISweden</td>
-<td style="text-align: right;">21</td>
+<td style="text-align: right;">22</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">posit-conf-2023</td>
@@ -802,7 +817,7 @@ <h1 class="title">Glittr stats</h1>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">bioinformatics-core-shared-training</td>
-<td style="text-align: right;">12</td>
+<td style="text-align: right;">13</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">bioinformatics-ca</td>
@@ -914,48 +929,48 @@ <h1 class="title">Glittr stats</h1>
 <tbody>
 <tr class="odd">
 <td style="text-align: left;">other</td>
-<td style="text-align: right;">220</td>
-<td style="text-align: right;">36.0</td>
+<td style="text-align: right;">222</td>
+<td style="text-align: right;">35.6</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">none</td>
-<td style="text-align: right;">184</td>
-<td style="text-align: right;">30.1</td>
+<td style="text-align: right;">188</td>
+<td style="text-align: right;">30.2</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">mit</td>
-<td style="text-align: right;">66</td>
-<td style="text-align: right;">10.8</td>
+<td style="text-align: right;">68</td>
+<td style="text-align: right;">10.9</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">cc-by-sa-4.0</td>
 <td style="text-align: right;">31</td>
-<td style="text-align: right;">5.1</td>
+<td style="text-align: right;">5.0</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">gpl-3.0</td>
 <td style="text-align: right;">30</td>
-<td style="text-align: right;">4.9</td>
+<td style="text-align: right;">4.8</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">cc-by-4.0</td>
-<td style="text-align: right;">28</td>
-<td style="text-align: right;">4.6</td>
+<td style="text-align: right;">29</td>
+<td style="text-align: right;">4.7</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">cc0-1.0</td>
 <td style="text-align: right;">25</td>
-<td style="text-align: right;">4.1</td>
+<td style="text-align: right;">4.0</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">apache-2.0</td>
 <td style="text-align: right;">12</td>
-<td style="text-align: right;">2.0</td>
+<td style="text-align: right;">1.9</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">bsd-3-clause</td>
-<td style="text-align: right;">9</td>
-<td style="text-align: right;">1.5</td>
+<td style="text-align: right;">12</td>
+<td style="text-align: right;">1.9</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">agpl-3.0</td>
@@ -1042,11 +1057,11 @@ <h1 class="title">Glittr stats</h1>
 <tbody>
 <tr class="odd">
 <td style="text-align: left;">undefined</td>
-<td style="text-align: right;">254</td>
+<td style="text-align: right;">262</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">United States</td>
-<td style="text-align: right;">146</td>
+<td style="text-align: right;">147</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">Canada</td>
@@ -1058,7 +1073,7 @@ <h1 class="title">Glittr stats</h1>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">Sweden</td>
-<td style="text-align: right;">22</td>
+<td style="text-align: right;">23</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">United Kingdom</td>
@@ -1078,7 +1093,7 @@ <h1 class="title">Glittr stats</h1>
 </tr>
 <tr class="even">
 <td style="text-align: left;">Netherlands</td>
-<td style="text-align: right;">11</td>
+<td style="text-align: right;">12</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">Portugal</td>
@@ -1133,10 +1148,14 @@ <h1 class="title">Glittr stats</h1>
 <td style="text-align: right;">1</td>
 </tr>
 <tr class="even">
-<td style="text-align: left;">Poland</td>
+<td style="text-align: left;">Mexico</td>
 <td style="text-align: right;">1</td>
 </tr>
 <tr class="odd">
+<td style="text-align: left;">Poland</td>
+<td style="text-align: right;">1</td>
+</tr>
+<tr class="even">
 <td style="text-align: left;">Ukraine</td>
 <td style="text-align: right;">1</td>
 </tr>