Built site for gh-pages

SydneyBioX · Nov 6, 2024 · 81e52fd · 81e52fd
1 parent e60f1c8
commit 81e52fd
Show file tree

Hide file tree

Showing 5 changed files with 14 additions and 4 deletions.
diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-89ba7ec4
+3083a05d
diff --git a/results/index.html b/results/index.html
diff --git a/search.json b/search.json
@@ -6,6 +6,13 @@
     "section": "",
     "text": "Evaluation\nTask\nSubTask\nTransformation\nMetric\nRange\n\n\n\n\nData properties\nSpot-level\nFraction zero\nNo\nKernel Density\n[0, infinity) then map to [0, 1]\n\n\n\n\nLibrary size\nNo\n\n\n\n\n\n\nTMM\nNo\n\n\n\n\n\n\nEffective library size\nNo\n\n\n\n\n\n\nScaled variance\nYes, z-score standardization\n\n\n\n\n\n\nScaled mean\nYes, z-score standardization\n\n\n\n\n\n\nLibrary size vs Fraction zero\nNo\n\n\n\n\n\n\nSample Pearson correlation\nNo\n\n\n\n\n\nGene-level\nFraction zero gene\nNo\n\n\n\n\n\n\nScaled variance\n\nYes, z-score standardization\n\n\n\n\n\nScaled mean\nYes, z-score standardization\n\n\n\n\n\n\nMean vs variance\nNo\n\n\n\n\n\n\nMean vs variance (scale)\n\nYes, log-normal transformation\n\n\n\n\n\nMean vs fraction zero\nNo\n\n\n\n\n\n\nGene Pearson correlation\nNo\n\n\n\n\n\nSpatial-level\nTransition Matrix (TM)\nNo\n\n\n\n\n\n\nNeighborhood enrichment matrix (NEM)\nNo\n\n\n\n\n\n\nCentralized score matrix (CSM)\nNo\n\n\n\n\n\n\nCell type interaction\nNo\n\n\n\n\n\n\nMoran’s I\nNo\n\n\n\n\n\n\nL statistics\nNo\n\n\n\n\n\n\nNearest neighbor correlation\nNo\n\n\n\n\nSpatial downstream analysis\nSpatial clustering\n\nNo\nAdjusted rand index (ARI)\n[-1, 1]\n\n\n\n\n\nNo\nNormalized mutual information (NMI)\n[0, 1]\n\n\n\nCell type deconvolution\n\nNo\nRoot mean square deviation (RMSE)\n[0, infinity)\n\n\n\n\n\nNo\nJensen-Shannon divergence (JSD)\n[0, 1]\n\n\n\nSpatially variable genes (SVG) identification\n\nNo\nPrecision\n[0, 1]\n\n\n\n\n\nNo\nRecall\n[0, 1]\n\n\n\nSpatial cross-correlation\n\nNo\nCosine similarity\n[-1, 1]\n\n\n\n\n\nNo\nMental statistics\n[-1, 1]\n\n\nScalability\n200 x 200\n\nNo\ntime\n[0, infinity)\n\n\n\n3k x 500\n\nNo\nmemory\n[0, infinity)\n\n\n\n5k x 1k"
   },
+  {
+    "objectID": "supplementary/index.html#details-of-the-three-evaluations-categories-with-metric-and-range-in-this-study",
+    "href": "supplementary/index.html#details-of-the-three-evaluations-categories-with-metric-and-range-in-this-study",
+    "title": "Supplementary",
+    "section": "",
+    "text": "Evaluation\nTask\nSubTask\nTransformation\nMetric\nRange\n\n\n\n\nData properties\nSpot-level\nFraction zero\nNo\nKernel Density\n[0, infinity) then map to [0, 1]\n\n\n\n\nLibrary size\nNo\n\n\n\n\n\n\nTMM\nNo\n\n\n\n\n\n\nEffective library size\nNo\n\n\n\n\n\n\nScaled variance\nYes, z-score standardization\n\n\n\n\n\n\nScaled mean\nYes, z-score standardization\n\n\n\n\n\n\nLibrary size vs Fraction zero\nNo\n\n\n\n\n\n\nSample Pearson correlation\nNo\n\n\n\n\n\nGene-level\nFraction zero gene\nNo\n\n\n\n\n\n\nScaled variance\n\nYes, z-score standardization\n\n\n\n\n\nScaled mean\nYes, z-score standardization\n\n\n\n\n\n\nMean vs variance\nNo\n\n\n\n\n\n\nMean vs variance (scale)\n\nYes, log-normal transformation\n\n\n\n\n\nMean vs fraction zero\nNo\n\n\n\n\n\n\nGene Pearson correlation\nNo\n\n\n\n\n\nSpatial-level\nTransition Matrix (TM)\nNo\n\n\n\n\n\n\nNeighborhood enrichment matrix (NEM)\nNo\n\n\n\n\n\n\nCentralized score matrix (CSM)\nNo\n\n\n\n\n\n\nCell type interaction\nNo\n\n\n\n\n\n\nMoran’s I\nNo\n\n\n\n\n\n\nL statistics\nNo\n\n\n\n\n\n\nNearest neighbor correlation\nNo\n\n\n\n\nSpatial downstream analysis\nSpatial clustering\n\nNo\nAdjusted rand index (ARI)\n[-1, 1]\n\n\n\n\n\nNo\nNormalized mutual information (NMI)\n[0, 1]\n\n\n\nCell type deconvolution\n\nNo\nRoot mean square deviation (RMSE)\n[0, infinity)\n\n\n\n\n\nNo\nJensen-Shannon divergence (JSD)\n[0, 1]\n\n\n\nSpatially variable genes (SVG) identification\n\nNo\nPrecision\n[0, 1]\n\n\n\n\n\nNo\nRecall\n[0, 1]\n\n\n\nSpatial cross-correlation\n\nNo\nCosine similarity\n[-1, 1]\n\n\n\n\n\nNo\nMental statistics\n[-1, 1]\n\n\nScalability\n200 x 200\n\nNo\ntime\n[0, infinity)\n\n\n\n3k x 500\n\nNo\nmemory\n[0, infinity)\n\n\n\n5k x 1k"
+  },
   {
     "objectID": "index.html",
     "href": "index.html",

diff --git a/sitemap.xml b/sitemap.xml
@@ -2,7 +2,7 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
     <loc>https://SydneyBioX.github.io/SpatialSimbench_website/supplementary/index.html</loc>
-    <lastmod>2024-11-06T06:48:30.162Z</lastmod>
+    <lastmod>2024-11-06T06:50:33.320Z</lastmod>
   </url>
   <url>
     <loc>https://SydneyBioX.github.io/SpatialSimbench_website/index.html</loc>

diff --git a/supplementary/index.html b/supplementary/index.html
@@ -134,6 +134,8 @@ <h1 class="title">Supplementary</h1>
 </header>
 
 
+<section id="details-of-the-three-evaluations-categories-with-metric-and-range-in-this-study" class="level2">
+<h2 class="anchored" data-anchor-id="details-of-the-three-evaluations-categories-with-metric-and-range-in-this-study">Details of the three evaluations categories with metric and range in this study</h2>
 <table class="caption-top table">
 <colgroup>
 <col style="width: 14%">
@@ -422,6 +424,7 @@ <h1 class="title">Supplementary</h1>
 </table>
 
 
+</section>
 
 </main> <!-- /main -->
 <script id="quarto-html-after-body" type="application/javascript">