version 1.3.5 pre-final build

GuyTeichman · May 26, 2020 · c7aab36 · c7aab36
1 parent a74d964
commit c7aab36
Show file tree

Hide file tree

Showing 156 changed files with 1,484 additions and 402 deletions.
diff --git a/docs/build/.buildinfo b/docs/build/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 4323fe273845a7633ab54c33f381be6b
+config: 04c7c8f107439a7d33b3255fcd84df35
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/.doctrees/environment.pickle b/docs/build/.doctrees/environment.pickle
diff --git a/docs/build/.doctrees/index.doctree b/docs/build/.doctrees/index.doctree
diff --git a/docs/build/_static/documentation_options.js b/docs/build/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.3.4',
+    VERSION: '1.3.5',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/build/authors.html b/docs/build/authors.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Credits &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>Credits &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 
@@ -38,8 +38,8 @@
   <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="History" href="history.html" />
-    <link rel="prev" title="User guide" href="user_guide.html" /> 
+    <link rel="next" title="Installation" href="installation.html" />
+    <link rel="prev" title="What is RNAlysis?" href="readme.html" /> 
 </head>
 
 <body class="wy-body-for-nav">
@@ -86,22 +86,31 @@
 
 
 
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p class="caption"><span class="caption-text">About RNAlysis:</span></p>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="readme.html">What is RNAlysis?</a></li>
 <li class="toctree-l1"><a class="reference internal" href="readme.html#main-features">Main Features</a></li>
 <li class="toctree-l1"><a class="reference internal" href="readme.html#dependencies">Dependencies</a></li>
 <li class="toctree-l1"><a class="reference internal" href="readme.html#where-to-get-it">Where to get it</a></li>
 <li class="toctree-l1"><a class="reference internal" href="readme.html#credits">Credits</a></li>
-<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="user_guide.html">User guide</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/GuyTeichman/RNAlysis">GitHub page</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Credits</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#development-lead">Development Lead</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#contributors">Contributors</a></li>
 </ul>
 </li>
+</ul>
+<p class="caption"><span class="caption-text">Starting with RNAlysis:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="user_guide.html">User guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="glossary.html">Glossary</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Change history:</span></p>
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="history.html">History</a></li>
 </ul>
+<p class="caption"><span class="caption-text">Modules:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="rnalysis.filtering.html">rnalysis.filtering</a></li>
 <li class="toctree-l1"><a class="reference internal" href="rnalysis.enrichment.html">rnalysis.enrichment</a></li>
@@ -196,10 +205,10 @@ <h2>Contributors<a class="headerlink" href="#contributors" title="Permalink to t
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
-        <a href="history.html" class="btn btn-neutral float-right" title="History" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="installation.html" class="btn btn-neutral float-right" title="Installation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
-        <a href="user_guide.html" class="btn btn-neutral float-left" title="User guide" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="readme.html" class="btn btn-neutral float-left" title="What is RNAlysis?" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>
 

diff --git a/docs/build/contributing.html b/docs/build/contributing.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Contributing &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>Contributing &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 
@@ -84,18 +84,27 @@
 
 
 
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p class="caption"><span class="caption-text">About RNAlysis:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="readme.html">What is RNAlysis?</a></li>
 <li class="toctree-l1"><a class="reference internal" href="readme.html#main-features">Main Features</a></li>
 <li class="toctree-l1"><a class="reference internal" href="readme.html#dependencies">Dependencies</a></li>
 <li class="toctree-l1"><a class="reference internal" href="readme.html#where-to-get-it">Where to get it</a></li>
 <li class="toctree-l1"><a class="reference internal" href="readme.html#credits">Credits</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/GuyTeichman/RNAlysis">GitHub page</a></li>
+<li class="toctree-l1"><a class="reference internal" href="authors.html">Credits</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Starting with RNAlysis:</span></p>
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="user_guide.html">User guide</a></li>
-<li class="toctree-l1"><a class="reference internal" href="authors.html">Credits</a></li>
+<li class="toctree-l1"><a class="reference internal" href="glossary.html">Glossary</a></li>
+</ul>
+<p class="caption"><span class="caption-text">Change history:</span></p>
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="history.html">History</a></li>
 </ul>
+<p class="caption"><span class="caption-text">Modules:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="rnalysis.filtering.html">rnalysis.filtering</a></li>
 <li class="toctree-l1"><a class="reference internal" href="rnalysis.enrichment.html">rnalysis.enrichment</a></li>

diff --git a/docs/build/genindex.html b/docs/build/genindex.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Index &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>Index &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/glossary.html b/docs/build/glossary.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Glossary &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>Glossary &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/history.html b/docs/build/history.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>History &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>History &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/index.html b/docs/build/index.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>RNAlysis 1.3.4 documentation &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>RNAlysis 1.3.5 documentation &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 
@@ -155,7 +155,7 @@
 
       <li><a href="#">Docs</a> &raquo;</li>
 
-      <li>RNAlysis 1.3.4 documentation</li>
+      <li>RNAlysis 1.3.5 documentation</li>
 
 
       <li class="wy-breadcrumbs-aside">
@@ -175,7 +175,7 @@
            <div itemprop="articleBody">
 
   <div class="section" id="rnalysis-release-documentation">
-<h1>RNAlysis 1.3.4 documentation<a class="headerlink" href="#rnalysis-release-documentation" title="Permalink to this headline">¶</a></h1>
+<h1>RNAlysis 1.3.5 documentation<a class="headerlink" href="#rnalysis-release-documentation" title="Permalink to this headline">¶</a></h1>
 <div class="toctree-wrapper compound">
 <p class="caption"><span class="caption-text">About RNAlysis:</span></p>
 <ul>

diff --git a/docs/build/installation.html b/docs/build/installation.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Installation &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>Installation &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 
@@ -104,6 +104,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="user_guide.html">User guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="glossary.html">Glossary</a></li>
 </ul>
 <p class="caption"><span class="caption-text">Change history:</span></p>
 <ul>

diff --git a/docs/build/objects.inv b/docs/build/objects.inv
diff --git a/docs/build/py-modindex.html b/docs/build/py-modindex.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Python Module Index &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>Python Module Index &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/readme.html b/docs/build/readme.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>What is RNAlysis? &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>What is RNAlysis? &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 
@@ -39,7 +39,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Credits" href="authors.html" />
-    <link rel="prev" title="RNAlysis 1.3.4 documentation" href="index.html" /> 
+    <link rel="prev" title="RNAlysis 1.3.5 documentation" href="index.html" /> 
 </head>
 
 <body class="wy-body-for-nav">
@@ -104,6 +104,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="user_guide.html">User guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="glossary.html">Glossary</a></li>
 </ul>
 <p class="caption"><span class="caption-text">Change history:</span></p>
 <ul>
@@ -267,7 +268,7 @@ <h2>Contributors<a class="headerlink" href="#contributors" title="Permalink to t
         <a href="authors.html" class="btn btn-neutral float-right" title="Credits" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
-        <a href="index.html" class="btn btn-neutral float-left" title="RNAlysis 1.3.4 documentation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="index.html" class="btn btn-neutral float-left" title="RNAlysis 1.3.5 documentation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.__init__.html b/docs/build/rnalysis.enrichment.FeatureSet.__init__.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.__init__ &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.__init__ &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.biotypes.html b/docs/build/rnalysis.enrichment.FeatureSet.biotypes.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.biotypes &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.biotypes &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.difference.html b/docs/build/rnalysis.enrichment.FeatureSet.difference.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.difference &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.difference &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.enrich_hypergeometric.html b/docs/build/rnalysis.enrichment.FeatureSet.enrich_hypergeometric.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.enrich_hypergeometric &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.enrich_hypergeometric &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.enrich_randomization.html b/docs/build/rnalysis.enrichment.FeatureSet.enrich_randomization.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.enrich_randomization &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.enrich_randomization &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.enrich_randomization_parallel.html b/docs/build/rnalysis.enrichment.FeatureSet.enrich_randomization_parallel.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.enrich_randomization_parallel &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.enrich_randomization_parallel &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.go_enrichment.html b/docs/build/rnalysis.enrichment.FeatureSet.go_enrichment.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.go_enrichment &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.go_enrichment &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.html b/docs/build/rnalysis.enrichment.FeatureSet.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.intersection.html b/docs/build/rnalysis.enrichment.FeatureSet.intersection.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.intersection &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.intersection &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.save_txt.html b/docs/build/rnalysis.enrichment.FeatureSet.save_txt.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.save_txt &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.save_txt &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.symmetric_difference.html b/docs/build/rnalysis.enrichment.FeatureSet.symmetric_difference.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.symmetric_difference &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.symmetric_difference &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.FeatureSet.union.html b/docs/build/rnalysis.enrichment.FeatureSet.union.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.FeatureSet.union &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.FeatureSet.union &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.html b/docs/build/rnalysis.enrichment.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.upset_plot.html b/docs/build/rnalysis.enrichment.upset_plot.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.upset_plot &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.upset_plot &mdash; RNAlysis 1.3.5 documentation</title>
 
 
 

diff --git a/docs/build/rnalysis.enrichment.venn_diagram.html b/docs/build/rnalysis.enrichment.venn_diagram.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>rnalysis.enrichment.venn_diagram &mdash; RNAlysis 1.3.4 documentation</title>
+  <title>rnalysis.enrichment.venn_diagram &mdash; RNAlysis 1.3.5 documentation</title>