add _quarto.yml

ocbe-uio · Mar 11, 2024 · d91ef95 · d91ef95
1 parent 6e64b7f
commit d91ef95
Show file tree

Hide file tree

Showing 52 changed files with 1,974 additions and 37 deletions.
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,5 @@
 GDCdata/
 MANIFEST.txt
 TCGA_data.rda
+
+/.quarto/
diff --git a/_quarto.yml b/_quarto.yml
@@ -0,0 +1,43 @@
+project:
+  type: website
+  output-dir: _site
+
+theme:
+  light: default
+  dark: [default, theme-dark.scss]
+
+website:
+  page-navigation: true
+  title: "Survive with Omics"
+  repo-url: https://github.com/ocbe-uio/survomics
+  repo-actions: [source, issue]
+
+  navbar:
+    background: light
+    search: true
+    tools:
+      - icon: github
+        menu:
+          - text: Source Code
+            url:  https://github.com/ocbe-uio/survomics
+          - text: Report a Bug
+            url:  https://github.com/ocbe-uio/survomics/issues/new
+
+
+format:
+  html:
+    grid: 
+      # body-width: 2000px
+      sidebar-width: 350px
+      margin-width: 350px
+    toc: true
+    code-overflow: wrap
+
+  # sidebar:
+  #   title: "Survive with Omics"
+  #   pinned: true
+  #   tools: 
+  #     - icon: github
+  #       href: https://github.com/ocbe-uio/survomics
+  #       text: "Survive with Omics repo"
+
diff --git a/_site/fig/TCGA_adaptiveLasso.png b/_site/fig/TCGA_adaptiveLasso.png
diff --git a/_site/fig/TCGA_bayesEN.png b/_site/fig/TCGA_bayesEN.png
diff --git a/_site/fig/TCGA_bayesLassoM.png b/_site/fig/TCGA_bayesLassoM.png
diff --git a/_site/fig/TCGA_bayesSpikeSlab.png b/_site/fig/TCGA_bayesSpikeSlab.png
diff --git a/_site/fig/TCGA_bayeslasso.png b/_site/fig/TCGA_bayeslasso.png
diff --git a/_site/fig/TCGA_elastic.png b/_site/fig/TCGA_elastic.png
diff --git a/_site/fig/TCGA_lasso.png b/_site/fig/TCGA_lasso.png
diff --git a/_site/fig/TCGA_pca.png b/_site/fig/TCGA_pca.png
diff --git a/_site/fig/TCGA_surv_auc_lasso.png b/_site/fig/TCGA_surv_auc_lasso.png
diff --git a/_site/fig/TCGA_surv_brier_lasso.png b/_site/fig/TCGA_surv_brier_lasso.png
diff --git a/_site/fig/TCGA_surv_brier_t_lasso.png b/_site/fig/TCGA_surv_brier_t_lasso.png
diff --git a/_site/fig/TCGA_surv_calibration.png b/_site/fig/TCGA_surv_calibration.png
diff --git a/_site/fig/TCGA_surv_cindex_lasso.png b/_site/fig/TCGA_surv_cindex_lasso.png
diff --git a/_site/fig/TCGA_surv_iauc_lasso.png b/_site/fig/TCGA_surv_iauc_lasso.png
diff --git a/_site/fig/TCGA_surv_km1.png b/_site/fig/TCGA_surv_km1.png
diff --git a/_site/fig/TCGA_surv_km2.png b/_site/fig/TCGA_surv_km2.png
diff --git a/_site/fig/TCGA_surv_km_lasso.png b/_site/fig/TCGA_surv_km_lasso.png
diff --git a/_site/fig/TCGA_surv_km_lasso2.png b/_site/fig/TCGA_surv_km_lasso2.png
diff --git a/_site/fig/TCGA_surv_nomogram.png b/_site/fig/TCGA_surv_nomogram.png
diff --git a/_site/fig/TCGA_surv_roc.png b/_site/fig/TCGA_surv_roc.png
diff --git a/_site/fig/TCGA_survival.png b/_site/fig/TCGA_survival.png
diff --git a/_site/fig/TCGA_tsne.png b/_site/fig/TCGA_tsne.png
diff --git a/_site/fig/TCGA_umap.png b/_site/fig/TCGA_umap.png
diff --git a/_site/fig/mlr3_calibration_BS.png b/_site/fig/mlr3_calibration_BS.png
diff --git a/_site/fig/mlr3_calibration_RCLL.png b/_site/fig/mlr3_calibration_RCLL.png
diff --git a/_site/fig/mlr3_discrimination_msrs.png b/_site/fig/mlr3_discrimination_msrs.png
diff --git a/_site/index.html b/_site/index.html
@@ -0,0 +1,8 @@
+<html xmlns="http://www.w3.org/1999/xhtml">    
+  <head>      
+    <title>Redirect to survomics.html</title>      
+    <meta http-equiv="refresh" content="0;URL='survomics.html'" />    
+  </head>    
+  <body> 
+  </body>  
+</html>     
diff --git a/_site/search.json b/_site/search.json
diff --git a/_site/site_libs/bootstrap/bootstrap-dark.min.css b/_site/site_libs/bootstrap/bootstrap-dark.min.css
diff --git a/..._files/libs/bootstrap/bootstrap-icons.css → ...e/site_libs/bootstrap/bootstrap-icons.css b/..._files/libs/bootstrap/bootstrap-icons.css → ...e/site_libs/bootstrap/bootstrap-icons.css
diff --git a/...files/libs/bootstrap/bootstrap-icons.woff → .../site_libs/bootstrap/bootstrap-icons.woff b/...files/libs/bootstrap/bootstrap-icons.woff → .../site_libs/bootstrap/bootstrap-icons.woff
diff --git a/_site/site_libs/bootstrap/bootstrap.min.css b/_site/site_libs/bootstrap/bootstrap.min.css
diff --git a/...ics_files/libs/bootstrap/bootstrap.min.js → _site/site_libs/bootstrap/bootstrap.min.js b/...ics_files/libs/bootstrap/bootstrap.min.js → _site/site_libs/bootstrap/bootstrap.min.js
diff --git a/...ics_files/libs/clipboard/clipboard.min.js → _site/site_libs/clipboard/clipboard.min.js b/...ics_files/libs/clipboard/clipboard.min.js → _site/site_libs/clipboard/clipboard.min.js
diff --git a/...mics_files/libs/quarto-html/anchor.min.js → _site/site_libs/quarto-html/anchor.min.js b/...mics_files/libs/quarto-html/anchor.min.js → _site/site_libs/quarto-html/anchor.min.js
diff --git a/...mics_files/libs/quarto-html/popper.min.js → _site/site_libs/quarto-html/popper.min.js b/...mics_files/libs/quarto-html/popper.min.js → _site/site_libs/quarto-html/popper.min.js
diff --git a/_site/site_libs/quarto-html/quarto-syntax-highlighting-dark.css b/_site/site_libs/quarto-html/quarto-syntax-highlighting-dark.css
diff --git a/...uarto-html/quarto-syntax-highlighting.css → ...uarto-html/quarto-syntax-highlighting.css b/...uarto-html/quarto-syntax-highlighting.css → ...uarto-html/quarto-syntax-highlighting.css
diff --git a/survomics_files/libs/quarto-html/quarto.js → _site/site_libs/quarto-html/quarto.js b/survomics_files/libs/quarto-html/quarto.js → _site/site_libs/quarto-html/quarto.js
diff --git a/survomics_files/libs/quarto-html/tippy.css → _site/site_libs/quarto-html/tippy.css b/survomics_files/libs/quarto-html/tippy.css → _site/site_libs/quarto-html/tippy.css
diff --git a/...s_files/libs/quarto-html/tippy.umd.min.js → _site/site_libs/quarto-html/tippy.umd.min.js b/...s_files/libs/quarto-html/tippy.umd.min.js → _site/site_libs/quarto-html/tippy.umd.min.js
diff --git a/_site/site_libs/quarto-nav/headroom.min.js b/_site/site_libs/quarto-nav/headroom.min.js