Removed .html suffix.

ayushnoori · May 20, 2021 · 18698c9 · 18698c9
1 parent 46330b3
commit 18698c9
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diff --git a/README.md b/README.md
@@ -5,23 +5,26 @@
 # Setup
 Install [R](https://www.r-project.org/) to run our code.
 
-# Code Availability
-Our codebase is available on GitHub at [mindds.github.io/apoe-glia](https://mindds.github.io/apoe-glia/) and below.
+# Documentation
+To read our documented code, please visit [mindds.github.io/apoe-glia](https://mindds.github.io/apoe-glia) or see below.
 
 ### Functions
-* [Models](https://mindds.github.io/apoe-glia/models.html)
-* [Spectral Clustering](https://mindds.github.io/apoe-glia/spectral-clustering.html)
+* [Models](https://mindds.github.io/apoe-glia/models)
+* [Spectral Clustering](https://mindds.github.io/apoe-glia/spectral-clustering)
 
 ### ROSMAP
-* [Define Variables](https://mindds.github.io/apoe-glia/ROSMAP-variables.html)
-* [Pre-Process Data](https://mindds.github.io/apoe-glia/ROSMAP-preprocess.html)
-* [Microglia Analysis](https://mindds.github.io/apoe-glia/ROSMAP-microglia.html)
-* [Astrocyte Analysis](https://mindds.github.io/apoe-glia/ROSMAP-astrocyte.html)
+* [Define Variables](https://mindds.github.io/apoe-glia/ROSMAP-variables)
+* [Pre-Process Data](https://mindds.github.io/apoe-glia/ROSMAP-preprocess)
+* [Microglia Analysis](https://mindds.github.io/apoe-glia/ROSMAP-microglia)
+* [Astrocyte Analysis](https://mindds.github.io/apoe-glia/ROSMAP-astrocyte)
 
 ### MSBB
-* [Define Variables](https://mindds.github.io/apoe-glia/MSBB-variables.html)
-* [Merge Data](https://mindds.github.io/apoe-glia/MSBB-merge.html)
-* [Microglia Analysis](https://mindds.github.io/apoe-glia/MSBB-microglia.html)
+* [Define Variables](https://mindds.github.io/apoe-glia/MSBB-variables)
+* [Merge Data](https://mindds.github.io/apoe-glia/MSBB-merge)
+* [Microglia Analysis](https://mindds.github.io/apoe-glia/MSBB-microglia)
 
 ### qPCR Analysis
-* [qPCR Analysis](https://mindds.github.io/apoe-glia/qPCR-analysis.html)
+* [qPCR Analysis](https://mindds.github.io/apoe-glia/qPCR-analysis)
+
+# Code Availability
+Our full codebase is available for download on [GitHub](https://github.com/mindds/apoe-glia).
diff --git a/_site.yml b/_site.yml
@@ -16,30 +16,30 @@ navbar:
     - text: "Functions"
       menu:
         - text: "Models"
-          href: models.html
+          href: models
         - text: "Spectral Clustering"
-          href: spectral-clustering.html
+          href: spectral-clustering
     - text: "ROSMAP"
       menu:
         - text: "Define Variables"
-          href: ROSMAP-variables.html
+          href: ROSMAP-variables
         - text: "Pre-Process Data"
-          href: ROSMAP-preprocess.html
+          href: ROSMAP-preprocess
         - text: "---"
         - text: "Microglia Analysis"
-          href: ROSMAP-microglia.html
+          href: ROSMAP-microglia
         - text: "---"
         - text: "Astrocyte Analysis"
-          href: ROSMAP-astrocyte.html
+          href: ROSMAP-astrocyte
     - text: "MSBB"
       menu:
         - text: "Define Variables"
-          href: MSBB-variables.html
+          href: MSBB-variables
         - text: "Merge Data"
-          href: MSBB-merge.html
+          href: MSBB-merge
         - text: "---"
         - text: "Microglia Analysis"
-          href: MSBB-microglia.html
+          href: MSBB-microglia
     - text: "qPCR"
-      href: qPCR-analysis.html
+      href: qPCR-analysis
 output: distill::distill_article
diff --git a/docs/404.html b/docs/404.html
@@ -2153,7 +2153,7 @@
     color: var(--hover-color, white);
   }</style>
   <!--/radix_placeholder_distill-->
-  <script src="site_libs/header-attrs-2.6/header-attrs.js"></script>
+  <script src="site_libs/header-attrs-2.8/header-attrs.js"></script>
   <script src="site_libs/popper-2.6.0/popper.min.js"></script>
   <link href="site_libs/tippy-6.2.7/tippy.css" rel="stylesheet" />
   <link href="site_libs/tippy-6.2.7/tippy-light-border.css" rel="stylesheet" />
@@ -2192,8 +2192,8 @@
 <span class="down-arrow">&#x25BE;</span>
 </button>
 <div class="nav-dropdown-content">
-<a href="models.html">Models</a>
-<a href="spectral-clustering.html">Spectral Clustering</a>
+<a href="models">Models</a>
+<a href="spectral-clustering">Spectral Clustering</a>
 </div>
 </div>
 <div class="nav-dropdown">
@@ -2203,12 +2203,12 @@
 <span class="down-arrow">&#x25BE;</span>
 </button>
 <div class="nav-dropdown-content">
-<a href="ROSMAP-variables.html">Define Variables</a>
-<a href="ROSMAP-preprocess.html">Pre-Process Data</a>
+<a href="ROSMAP-variables">Define Variables</a>
+<a href="ROSMAP-preprocess">Pre-Process Data</a>
 <hr/>
-<a href="ROSMAP-microglia.html">Microglia Analysis</a>
+<a href="ROSMAP-microglia">Microglia Analysis</a>
 <hr/>
-<a href="ROSMAP-astrocyte.html">Astrocyte Analysis</a>
+<a href="ROSMAP-astrocyte">Astrocyte Analysis</a>
 </div>
 </div>
 <div class="nav-dropdown">
@@ -2218,13 +2218,13 @@
 <span class="down-arrow">&#x25BE;</span>
 </button>
 <div class="nav-dropdown-content">
-<a href="MSBB-variables.html">Define Variables</a>
-<a href="MSBB-merge.html">Merge Data</a>
+<a href="MSBB-variables">Define Variables</a>
+<a href="MSBB-merge">Merge Data</a>
 <hr/>
-<a href="MSBB-microglia.html">Microglia Analysis</a>
+<a href="MSBB-microglia">Microglia Analysis</a>
 </div>
 </div>
-<a href="qPCR-analysis.html">qPCR</a>
+<a href="qPCR-analysis">qPCR</a>
 <a href="https://github.com/mindds/apoe-glia" aria-label="Link to source">
 <i class="fab fa-github" aria-hidden="true"></i>
 </a>

diff --git a/docs/MSBB-merge.html b/docs/MSBB-merge.html
@@ -2156,7 +2156,7 @@
     color: var(--hover-color, white);
   }</style>
   <!--/radix_placeholder_distill-->
-  <script src="site_libs/header-attrs-2.6/header-attrs.js"></script>
+  <script src="site_libs/header-attrs-2.8/header-attrs.js"></script>
   <script src="site_libs/popper-2.6.0/popper.min.js"></script>
   <link href="site_libs/tippy-6.2.7/tippy.css" rel="stylesheet" />
   <link href="site_libs/tippy-6.2.7/tippy-light-border.css" rel="stylesheet" />
@@ -2195,8 +2195,8 @@
 <span class="down-arrow">&#x25BE;</span>
 </button>
 <div class="nav-dropdown-content">
-<a href="models.html">Models</a>
-<a href="spectral-clustering.html">Spectral Clustering</a>
+<a href="models">Models</a>
+<a href="spectral-clustering">Spectral Clustering</a>
 </div>
 </div>
 <div class="nav-dropdown">
@@ -2206,12 +2206,12 @@
 <span class="down-arrow">&#x25BE;</span>
 </button>
 <div class="nav-dropdown-content">
-<a href="ROSMAP-variables.html">Define Variables</a>
-<a href="ROSMAP-preprocess.html">Pre-Process Data</a>
+<a href="ROSMAP-variables">Define Variables</a>
+<a href="ROSMAP-preprocess">Pre-Process Data</a>
 <hr/>
-<a href="ROSMAP-microglia.html">Microglia Analysis</a>
+<a href="ROSMAP-microglia">Microglia Analysis</a>
 <hr/>
-<a href="ROSMAP-astrocyte.html">Astrocyte Analysis</a>
+<a href="ROSMAP-astrocyte">Astrocyte Analysis</a>
 </div>
 </div>
 <div class="nav-dropdown">
@@ -2221,13 +2221,13 @@
 <span class="down-arrow">&#x25BE;</span>
 </button>
 <div class="nav-dropdown-content">
-<a href="MSBB-variables.html">Define Variables</a>
-<a href="MSBB-merge.html">Merge Data</a>
+<a href="MSBB-variables">Define Variables</a>
+<a href="MSBB-merge">Merge Data</a>
 <hr/>
-<a href="MSBB-microglia.html">Microglia Analysis</a>
+<a href="MSBB-microglia">Microglia Analysis</a>
 </div>
 </div>
-<a href="qPCR-analysis.html">qPCR</a>
+<a href="qPCR-analysis">qPCR</a>
 <a href="https://github.com/mindds/apoe-glia" aria-label="Link to source">
 <i class="fab fa-github" aria-hidden="true"></i>
 </a>
@@ -2263,7 +2263,7 @@ <h1 id="dependencies">Dependencies</h1>
 <p>Load requisite packages.</p>
 <div class="layout-chunk" data-layout="l-body">
 <div class="sourceCode">
-<pre class="sourceCode r"><code class="sourceCode r"><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://Rdatatable.gitlab.io/data.table'>data.table</a></span><span class='op'>)</span>
+<pre class="sourceCode r"><code class="sourceCode r"><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>data.table</span><span class='op'>)</span>
 <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>sva</span><span class='op'>)</span>
 </code></pre>
 </div>