Update files and cytoscape snapshots to match current versions.

workflows/rna_seq_to_enrichment_map/identify_pathways/index.html

@@ -309,7 +309,6 @@ <h4 id="software-requirements">Software requirements</h4>
 <p>We are opting to use the desktop version of GSEA. There are some hoops to jump through in order to get it:</p>
 
 <ol>
-  <li>Install <a href="http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html" target="_blank">Java version 8</a></li>
   <li><a href="http://software.broadinstitute.org/gsea/register.jsp" target="_blank">Register</a> to use the GSEA software</li>
   <li><a href="http://software.broadinstitute.org/gsea/login.jsp" target="_blank">Login</a></li>
   <li><a href="http://software.broadinstitute.org/gsea/downloads.jsp" target="_blank">Download</a></li>
@@ -331,13 +330,13 @@ <h4 id="ranked-gene-list">Ranked gene list</h4>
 
 <p>This is the output from the previous step.</p>
 
-<p><a href="/guide" role="button" class="btn btn-secondary btn-lg btn-block" download="">Ranks (.rnk)</a></p>
+<p><a href="/guide/workflows/rna_seq_to_enrichment_map/process_data/brca_hd_tep_ranks.rnk" role="button" class="btn btn-secondary btn-lg btn-block" download="">Ranks (.rnk)</a></p>
 
 <h4 id="gene-set-database">Gene set database</h4>
 
-<p>This is the human gene set database culled from various sources, generated by the Bader lab (<code class="highlighter-rouge">Human_GOBP_AllPathways_no_GO_iea_February_01_2017_symbol.gmt</code>).</p>
+<p>This is the human gene set database culled from various sources, <a href="https://download.baderlab.org/EM_Genesets/">generated by the Bader lab</a>.</p>
 
-<p><a href="Human_GOBP_AllPathways_no_GO_iea_February_01_2017_symbol.gmt.zip" role="button" class="btn btn-secondary btn-lg btn-block" download="">Gene Set Database (.gmt)</a></p>
+<p><a href="Human_GOBP_AllPathways_noPFOCR_no_GO_iea_April_01_2024_symbol.gmt" role="button" class="btn btn-secondary btn-lg btn-block" download="">Gene Set Database (.gmt)</a></p>
 
 <hr />
 
@@ -347,7 +346,7 @@ <h4 id="gene-set-database">Gene set database</h4>
 |--- input
 |    |
 |    |--- brca_hd_tep_ranks.rnk
-|    |--- Human_GOBP_AllPathways_no_GO_iea_February_01_2017_symbol.gmt
+|    |--- Human_GOBP_AllPathways_noPFOCR_no_GO_iea_&lt;date&gt;_symbol.gmt
 ...
 </code></pre></div></div>
 
@@ -384,7 +383,7 @@ <h4 id="2--settings">2.  Settings</h4>
   <li><code class="highlighter-rouge">Required fields</code>
     <ul>
       <li><code class="highlighter-rouge">Gene sets database</code>: Click the ellipsis and wait a few moments for a dialog to pop up. Navigate to <code class="highlighter-rouge">Gene matrix (local gmx/gmt)</code> (click arrow along top). Select the gene set database that you obtained above (<code class="highlighter-rouge">.gmt</code> file)</li>
-      <li><code class="highlighter-rouge">Collapse dataset to gene symbols</code>: False
+      <li><code class="highlighter-rouge">Collapse/Remap to gene symbols</code>: No_Collapse
         <ul>
           <li>This option is a vestige of microarray technology where an additional step was necessary to match array probes/spots to a single gene identifier.</li>
         </ul>
@@ -412,16 +411,6 @@ <h4 id="3-run-gsea">3. Run GSEA</h4>
 
 <p>Click <code class="highlighter-rouge">Run</code> in the <code class="highlighter-rouge">Run Gsea on a Pre-Ranked gene list</code> tab. The <code class="highlighter-rouge">GSEA reports</code> panel (Figure 5, bottom left) will show the <code class="highlighter-rouge">Name</code> of this run and the <code class="highlighter-rouge">Status</code> as <code class="highlighter-rouge">Running</code> while in progress.</p>
 
-<ul>
-  <li class="aside">
-    <h4 id="typical-run-times">Typical run times</h4>
-
-    <ul>
-      <li>Mac: MacBook Air (Early 2015), 2.2 GHz Intel Core i7, 8 GB 1600 MHz DDR3, OS X El Capitan (10.11.6) ~ 10 minutes</li>
-    </ul>
-  </li>
-</ul>
-
 <h4 id="4-post-gsea">4. Post-GSEA</h4>
 
 <p>Take a look at the directory you set for <code class="highlighter-rouge">Save results in this folder</code>. The default location is <code class="highlighter-rouge">gsea_home</code> in your user space. You should see something like the following:</p>
@@ -430,21 +419,21 @@ <h4 id="4-post-gsea">4. Post-GSEA</h4>
 |--- input
 |    |
 |    |--- brca_hd_tep_ranks.rnk
-|    |--- Human_GOBP_AllPathways_no_GO_iea_February_01_2017_symbol.gmt
+|    |--- Human_GOBP_AllPathways_noPFOCR_no_GO_iea_&lt;date&gt;_symbol.gmt
 |
 |--- gsea_home
     |
     |--- output
         |
-        |--- monthDay
+        |--- &lt;monthDay&gt;
             |
             |--- tep_brca_vs_hd.GseaPreranked.XXXXXXXXXXXXX
                 |
                 |--- index.html
                 |--- pos_snapshot.html
                 |--- neg_snapshot.html
-                |--- gsea_report_for_na_pos_XXXXXXXXXXXXX.xls
-                |--- gsea_report_for_na_neg_XXXXXXXXXXXXX.xls
+                |--- gsea_report_for_na_pos_XXXXXXXXXXXXX.tsv
+                |--- gsea_report_for_na_neg_XXXXXXXXXXXXX.tsv
                 |--- my_analysis.GseaPreranked.XXXXXXXXXXXXX.rpt
                 ...
 ...
@@ -491,7 +480,7 @@ <h5 id="enrichment-in-phenotype">Enrichment in phenotype</h5>
 
 <ul>
   <li>
-    <p><strong>Detailed enrichment results.</strong> These are the end-goal for our workflow step! These files provide a summary report of gene sets enriched in this phenotype. You can find these files inside your GSEA results folder named <code class="highlighter-rouge">gsea_report_for_na_pos_XXXXXXXXXXXXX.xls</code> and <code class="highlighter-rouge">gsea_report_for_na_neg_XXXXXXXXXXXXX.xls</code>. The rows of the report include information for each enriched gene set (Table 2).</p>
+    <p><strong>Detailed enrichment results.</strong> These are the end-goal for our workflow step! These files provide a summary report of gene sets enriched in this phenotype. You can find these files inside your GSEA results folder named <code class="highlighter-rouge">gsea_report_for_na_pos_XXXXXXXXXXXXX.tsv</code> and <code class="highlighter-rouge">gsea_report_for_na_neg_XXXXXXXXXXXXX.tsv</code>. The rows of the report include information for each enriched gene set (Table 2).</p>
 
     <p><strong>Table 2. Excerpt of enrichment report for BrCa class</strong></p>
 
@@ -578,11 +567,11 @@ <h4 id="enrichment-map-dependencies">Enrichment Map dependencies</h4>
 <ol>
   <li>
     <p>Enrichment report for BrCa
-  <a href="gsea_report_for_brca.xls" role="button" class="btn btn-secondary btn-lg btn-block" download="">BrCa report (.xls)</a></p>
+  <a href="gsea_report_for_brca.tsv" role="button" class="btn btn-secondary btn-lg btn-block" download="">BrCa report (.tsv)</a></p>
   </li>
   <li>
     <p>Enrichment report for HD
-  <a href="gsea_report_for_hd.xls" role="button" class="btn btn-secondary btn-lg btn-block" download="">HD report (.xls)</a></p>
+  <a href="gsea_report_for_hd.tsv" role="button" class="btn btn-secondary btn-lg btn-block" download="">HD report (.tsv)</a></p>
   </li>
 </ol>
 

workflows/rna_seq_to_enrichment_map/visualize/index.html

@@ -238,7 +238,7 @@ <h3 id="a-long-list-of-pathways">A long list of pathways</h3>
   </tbody>
 </table>
 
-<p>Notice that even under fairly stringent criteria (i.e. p-value &lt; 1%), there are a still 578 gene sets that are deemed significantly enriched in BrCa platelets and 394 in HD. Furthermore, our GSEA report declares that 8 191 genes were used as input in our ranked list. Have we simply kicked the can down the road and traded a long list of ~8 200 genes for a long list of ~1 000 gene sets?</p>
+<p>Notice that even under fairly stringent criteria (i.e. p-value &lt; 1%), there are a still hundreds of gene sets that are deemed significantly enriched in BrCa platelets and HD. Furthermore, our GSEA report declares that thousands of genes were used as input in our ranked list. Have we simply kicked the can down the road and traded a long list of thousands of genes for a long list of gene sets?</p>
 
 <h3 id="data-reduction">Data reduction</h3>
 
@@ -287,18 +287,17 @@ <h2 id="iii-workflow-step"><a href="#workflow_step" name="workflow_step">III. Wo
 <h4 id="software-requirements">Software requirements</h4>
 
 <ul>
-  <li>Install <a href="http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html" target="_blank">Java version 8</a></li>
   <li><a href="http://www.cytoscape.org/" target="_blank">Cytoscape</a>: version 3 or higher
     <ul>
       <li>Cytoscape is an indispensable tool for network visualization and analysis. The desktop software comes as a base installation and additional capabilities are added in the form of a large ecosystem of plugins or <a href="http://apps.cytoscape.org/" target="_blank">apps</a>. Checkout the <a href="http://manual.cytoscape.org/en/stable/index.html" target="_blank">Cytoscape User Manual</a> for full description of function and capabilities.</li>
     </ul>
   </li>
   <li>Cytoscape apps
     <ul>
-      <li><a href="http://apps.cytoscape.org/apps/enrichmentmap" target="_blank">Enrichment Map</a>: version 3.1.0</li>
-      <li><a href="http://apps.cytoscape.org/apps/clustermaker2" target="_blank">ClusterMaker2</a>: version 1.2.1</li>
-      <li><a href="http://apps.cytoscape.org/apps/wordcloud" target="_blank">WordCloud</a>: version 3.1.1</li>
-      <li><a href="http://apps.cytoscape.org/apps/autoannotate" target="_blank">AutoAnnotate</a>: version 1.2</li>
+      <li><a href="http://apps.cytoscape.org/apps/enrichmentmap" target="_blank">Enrichment Map</a></li>
+      <li><a href="http://apps.cytoscape.org/apps/clustermaker2" target="_blank">ClusterMaker2</a></li>
+      <li><a href="http://apps.cytoscape.org/apps/wordcloud" target="_blank">WordCloud</a></li>
+      <li><a href="http://apps.cytoscape.org/apps/autoannotate" target="_blank">AutoAnnotate</a></li>
     </ul>
   </li>
 </ul>
@@ -307,7 +306,7 @@ <h5 id="loading-apps">Loading apps</h5>
 
 <p>The base Cytoscape installation will use a collection of apps to generate the Enrichment Map. Apps are loaded into Cytoscape using the built-in App Manager.</p>
 
-<p>From the Cytoscape menu bar, select <code class="highlighter-rouge">'Apps' --&gt; 'App Manager'</code> to bring up an app search panel (Figure 4).</p>
+<p>From the Cytoscape menu bar, select <code class="highlighter-rouge">'Apps' --&gt; 'App Store' --&gt; 'Show App Store'</code> to bring up an app search panel (Figure 4).</p>
 
 <p><img src="figure_visualize_cytoscape_apps_em.png" alt="image" /></p>
 <div class="card bg-light">
@@ -318,7 +317,7 @@ <h5 id="loading-apps">Loading apps</h5>
   </div>
 </div>
 
-<p>Search for the app, highlight the correct search result and click <code class="highlighter-rouge">Install</code>. If the installation was successful, you should be able to select it by name in the <code class="highlighter-rouge">Apps</code> menu bar drop-down. Also, if you bring up the <code class="highlighter-rouge">App Manager</code> you should see it as a listing under the <code class="highlighter-rouge">Currently Installed</code> tab.</p>
+<p>Search for the app and install. If the installation was successful it will appear under <code class="highlighter-rouge">Installed apps</code>.</p>
 
 <hr />
 
@@ -341,25 +340,25 @@ <h3 id="input">Input</h3>
 
 <h4 id="gmt-file">GMT File</h4>
 
-<p><a href="/guide/" role="button" class="btn btn-secondary btn-lg btn-block" download=""> Gene Set Database (.gmt)</a></p>
+<p><a href="/guide//workflows/rna_seq_to_enrichment_map/identify_pathways/Human_GOBP_AllPathways_noPFOCR_no_GO_iea_April_01_2024_symbol.gmt" role="button" class="btn btn-secondary btn-lg btn-block" download=""> Gene Set Database (.gmt)</a></p>
 
 <h4 id="expression">Expression</h4>
 
-<p><a href="/guide/" role="button" class="btn btn-secondary btn-lg btn-block" download=""> Expression (.txt)</a></p>
+<p><a href="/guide//workflows/rna_seq_to_enrichment_map/process_data/brca_hd_tep_expression.txt" role="button" class="btn btn-secondary btn-lg btn-block" download=""> Expression (.txt)</a></p>
 
 <h4 id="enrichments">Enrichments</h4>
 
-<p><a href="/guide/" role="button" class="btn btn-secondary btn-lg btn-block" download=""> BrCa report (.xls)</a></p>
+<p><a href="/guide//workflows/rna_seq_to_enrichment_map/identify_pathways/gsea_report_for_brca.tsv" role="button" class="btn btn-secondary btn-lg btn-block" download=""> BrCa report (.tsv)</a></p>
 
-<p><a href="/guide/" role="button" class="btn btn-secondary btn-lg btn-block" download=""> HD report (.xls)</a></p>
+<p><a href="/guide//workflows/rna_seq_to_enrichment_map/identify_pathways/gsea_report_for_hd.tsv" role="button" class="btn btn-secondary btn-lg btn-block" download=""> HD report (.tsv)</a></p>
 
 <h4 id="ranks">Ranks</h4>
 
-<p><a href="/guide/" role="button" class="btn btn-secondary btn-lg btn-block" download=""> Ranks (.rnk)</a></p>
+<p><a href="/guide//workflows/rna_seq_to_enrichment_map/process_data/brca_hd_tep_ranks.rnk" role="button" class="btn btn-secondary btn-lg btn-block" download=""> Ranks (.rnk)</a></p>
 
 <h4 id="classes">Classes</h4>
 
-<p><a href="/guide/" role="button" class="btn btn-secondary btn-lg btn-block" download=""> Phenotype (.cls)</a></p>
+<p><a href="/guide//workflows/rna_seq_to_enrichment_map/process_data/brca_hd_tep_phenotype.cls" role="button" class="btn btn-secondary btn-lg btn-block" download=""> Phenotype (.cls)</a></p>
 
 <h3 id="analysis">Analysis</h3>