fix the index page

lishensuo · Jul 27, 2024 · af4fba9 · af4fba9
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diff --git a/.Rproj.user/65FDE9DB/bookdown-crossref/index.Rmd.xref b/.Rproj.user/65FDE9DB/bookdown-crossref/index.Rmd.xref
@@ -3,4 +3,5 @@ h1:cover-image-path-to-the-social-sharing-image-like-imagescover.jpg cover-image
 h1:about About
 h4:part-ⅰ Part Ⅰ
 h4:part-ⅱ Part Ⅱ
+h4:part-ⅲ Part Ⅲ
 
diff --git a/.Rproj.user/65FDE9DB/sources/prop/INDEX b/.Rproj.user/65FDE9DB/sources/prop/INDEX
@@ -1,9 +1,11 @@
 C%3A%2FUsers%2Fxiaoxin%2FDesktop%2FProject%2FUCSC%2FUCSC-develop%2FUCSCXenaShiny%2FR%2Ftcga_surv.R="F24CFC42"
+C%3A%2FUsers%2Fxiaoxin%2FDesktop%2FProject%2FUCSC%2Fbookdown%2Fdevelop%2FUCSCXenaShiny_Book%2F03-pkg-1-intro.Rmd="E000A4F2"
 C%3A%2FUsers%2Fxiaoxin%2FDesktop%2FProject%2FUCSC%2Fbookdown%2Fdevelop%2FUCSCXenaShiny_Book%2F06-pkg-4-analyze.Rmd="3CE5B23F"
 C%3A%2FUsers%2Fxiaoxin%2FDesktop%2FProject%2FUCSC%2Fbookdown%2Fdevelop%2FUCSCXenaShiny_Book%2F08-app-home.Rmd="18034169"
 C%3A%2FUsers%2Fxiaoxin%2FDesktop%2FProject%2FUCSC%2Fbookdown%2Fdevelop%2FUCSCXenaShiny_Book%2F11-app-customTPC.Rmd="E0B0B72F"
 C%3A%2FUsers%2Fxiaoxin%2FDesktop%2FProject%2FUCSC%2Fbookdown%2Fdevelop%2FUCSCXenaShiny_Book%2F12-app-personalTPC-1.Rmd="662F669F"
 C%3A%2FUsers%2Fxiaoxin%2FDesktop%2FProject%2FUCSC%2Fbookdown%2Fdevelop%2FUCSCXenaShiny_Book%2F13-app-personalTPC-2.Rmd="831F9DA1"
+C%3A%2FUsers%2Fxiaoxin%2FDesktop%2FProject%2FUCSC%2Fbookdown%2Fdevelop%2FUCSCXenaShiny_Book%2Findex.Rmd="D1F7EAED"
 C%3A%2FUsers%2Fxiaoxin%2FDesktop%2FProject%2FUCSC%2Fbookdown%2Fscript.r="D4F11159"
 C%3A%2FUsers%2Fxiaoxin%2FDesktop%2Fbookdown%2Fdevelop%2FUCSCXenaShiny_Book%2F02-background.Rmd="A6585E52"
 C%3A%2FUsers%2Fxiaoxin%2FDesktop%2Fbookdown%2Fdevelop%2FUCSCXenaShiny_Book%2F03-pkg-1-intro.Rmd="2A8A33EC"

diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
@@ -1,7 +1,9 @@
 C:/Users/xiaoxin/Desktop/Project/UCSC/UCSC-develop/UCSCXenaShiny/R/tcga_surv.R="78D57B31"
+C:/Users/xiaoxin/Desktop/Project/UCSC/bookdown/develop/UCSCXenaShiny_Book/03-pkg-1-intro.Rmd="635993D6"
 C:/Users/xiaoxin/Desktop/Project/UCSC/bookdown/develop/UCSCXenaShiny_Book/06-pkg-4-analyze.Rmd="3CE82B95"
 C:/Users/xiaoxin/Desktop/Project/UCSC/bookdown/develop/UCSCXenaShiny_Book/08-app-home.Rmd="66769C44"
 C:/Users/xiaoxin/Desktop/Project/UCSC/bookdown/develop/UCSCXenaShiny_Book/11-app-customTPC.Rmd="DC5637CB"
 C:/Users/xiaoxin/Desktop/Project/UCSC/bookdown/develop/UCSCXenaShiny_Book/12-app-personalTPC-1.Rmd="1C96D295"
 C:/Users/xiaoxin/Desktop/Project/UCSC/bookdown/develop/UCSCXenaShiny_Book/13-app-personalTPC-2.Rmd="3D5E3380"
+C:/Users/xiaoxin/Desktop/Project/UCSC/bookdown/develop/UCSCXenaShiny_Book/index.Rmd="50EDE2B3"
 C:/Users/xiaoxin/Desktop/Project/UCSC/bookdown/script.r="8ECEC38A"
diff --git a/docs/404.html b/docs/404.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/build-in.html b/docs/build-in.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/custom-tpc.html b/docs/custom-tpc.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/data-analysis.html b/docs/data-analysis.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/data-query.html b/docs/data-query.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/download.html b/docs/download.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/general-da.html b/docs/general-da.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/home.html b/docs/home.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/images/p0000_1.png b/docs/images/p0000_1.png
diff --git a/docs/images/p0000_2.png b/docs/images/p0000_2.png
diff --git a/docs/index.html b/docs/index.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -361,12 +361,12 @@ <h1>
 <div id="header">
 <h1 class="title">UCSCXenaShiny v2 Book</h1>
 <p class="author"><em>Shensuo Li, Shixiang Wang</em></p>
-<p class="date"><em>2024-07-08</em></p>
+<p class="date"><em>2024-07-27</em></p>
 </div>
 <div id="about" class="section level1 unnumbered hasAnchor">
 <h1>About<a href="index.html#about" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p><strong>UCSCXenaShiny</strong> is an R package for interactively exploring UCSC Xena datasets. It is mainly designed to provide a web app (built on the top of <a href="https://shiny.rstudio.com/"><code>{shiny}</code></a> framework and <a href="https://github.com/ropensci/UCSCXenaTools/"><code>{UCSCXenaTools}</code></a> package) for downloading, analyzing and visualizing datasets from <a href="https://xenabrowser.net/datapages/">UCSC Xena</a>. In the latest version, the application can support both general and personalized tumor molecular analysis with versatile functional modules and user-friendly interface layouts. Overall, our tool aims to make best use of public omics data from UCSC Xena and assist broad user community with precision oncology research.</p>
-<p><img src="images/p0000.png" width="80%" style="display: block; margin: auto;" /></p>
+<p><img src="images/p0000_1.png" width="100%" style="display: block; margin: auto;" /></p>
 <p>Here, we have prepared the tutorial book to introduce the detailed usage of UCSCXenaShiny based on R Markdown and <a href="https://github.com/rstudio/bookdown">bookdown</a>. Firstly, we will start with the basic knowledge of UCSC Xena repository and its data hubs in <strong>Chapter <a href="intro.html#intro">1</a></strong>. Then, the following chapters can be generally divided into two parts for the usage of R package and Shiny App:</p>
 <div id="part-ⅰ" class="section level4 unnumbered hasAnchor">
 <h4>Part Ⅰ<a href="index.html#part-ⅰ" class="anchor-section" aria-label="Anchor link to header"></a></h4>
@@ -389,6 +389,22 @@ <h4>Part Ⅱ<a href="index.html#part-ⅱ" class="anchor-section" aria-label="Anc
 <li><strong>Chapter <a href="per-tpc-2.html#per-tpc-2">12</a></strong>：The versatile analyses of personalized TPC pipelines.</li>
 <li><strong>Chapter <a href="download.html#download">13</a></strong>：Two download modules for the custom data subset.</li>
 </ul>
+</div>
+<div id="part-ⅲ" class="section level4 unnumbered hasAnchor">
+<h4>Part Ⅲ<a href="index.html#part-ⅲ" class="anchor-section" aria-label="Anchor link to header"></a></h4>
+<p>We have recorded a series of tutorial videos with step-by-step instructions:</p>
+<p><strong>1. English version</strong></p>
+<ul>
+<li>Episode 1-4: <a href="https://www.youtube.com/watch?v=VnIlzcVB1Ow&amp;list=PLN1jxcOQONG6pH8zvHr-qhI3MMtvluITf" class="uri">https://www.youtube.com/watch?v=VnIlzcVB1Ow&amp;list=PLN1jxcOQONG6pH8zvHr-qhI3MMtvluITf</a></li>
+</ul>
+<p><img src="images/p0000_2.png" width="90%" style="display: block; margin: auto;" /></p>
+<p><strong>2. Chinese version</strong></p>
+<ul>
+<li>Episode 1: <a href="https://www.bilibili.com/video/BV1rT421k7Zv" class="uri">https://www.bilibili.com/video/BV1rT421k7Zv</a></li>
+<li>Episode 2: <a href="https://www.bilibili.com/video/BV1E14218779" class="uri">https://www.bilibili.com/video/BV1E14218779</a></li>
+<li>Episode 3: <a href="https://www.bilibili.com/video/BV141421t71g" class="uri">https://www.bilibili.com/video/BV141421t71g</a></li>
+<li>Episode 4: <a href="https://www.bilibili.com/video/BV1TZ421K7VH" class="uri">https://www.bilibili.com/video/BV1TZ421K7VH</a></li>
+</ul>
 <hr />
 <p>Welcome to cite the following articles when <strong>UCSCXenaShiny</strong> has facilitated your study:</p>
 <ol style="list-style-type: decimal">

diff --git a/docs/install.html b/docs/install.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/intro.html b/docs/intro.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/per-tpc-1.html b/docs/per-tpc-1.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/per-tpc-2.html b/docs/per-tpc-2.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
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diff --git a/docs/repo.html b/docs/repo.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
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diff --git a/docs/search_index.json b/docs/search_index.json
diff --git a/docs/visit.html b/docs/visit.html
@@ -29,7 +29,7 @@
 <meta name="author" content="Shensuo Li, Shixiang Wang" />
 
 
-<meta name="date" content="2024-07-08" />
+<meta name="date" content="2024-07-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/images/p0000_1.png b/images/p0000_1.png
diff --git a/images/p0000_2.png b/images/p0000_2.png
diff --git a/index.Rmd b/index.Rmd
@@ -21,8 +21,8 @@ github-repo: rstudio/bookdown-demo
 
 **UCSCXenaShiny** is an R package for interactively exploring UCSC Xena datasets. It is mainly designed to provide a web app (built on the top of [`{shiny}`](https://shiny.rstudio.com/) framework and [`{UCSCXenaTools}`](https://github.com/ropensci/UCSCXenaTools/) package) for downloading, analyzing and visualizing datasets from [UCSC Xena](https://xenabrowser.net/datapages/). In the latest version, the application can support both general and personalized  tumor molecular analysis with versatile functional modules and user-friendly interface layouts. Overall, our tool aims to make best use of public omics data from UCSC Xena and assist broad user community with precision oncology research.  
 
-```{r p0000,  fig.align='center', echo = FALSE, out.width="80%"}
-knitr::include_graphics('images/p0000.png')
+```{r p0000_1,  fig.align='center', echo = FALSE, out.width="100%"}
+knitr::include_graphics('images/p0000_1.png')
 ```
 
 Here, we have prepared the tutorial book to introduce the detailed usage of UCSCXenaShiny based on R Markdown and [bookdown](https://github.com/rstudio/bookdown). Firstly, we will start with the basic knowledge of UCSC Xena repository and its data hubs in **Chapter \@ref(intro)**. Then, the following chapters can be generally divided into two parts for the usage of R package and Shiny App:
@@ -47,7 +47,25 @@ Here, we have prepared the tutorial book to introduce the detailed usage of UCSC
 
 
 
+#### Part Ⅲ {-} 
 
+We have recorded a series of tutorial videos with step-by-step instructions:
+
+**1. English version**
+
+- Episode 1-4: https://www.youtube.com/watch?v=VnIlzcVB1Ow&list=PLN1jxcOQONG6pH8zvHr-qhI3MMtvluITf
+
+
+```{r p0000_2,  fig.align='center', echo = FALSE, out.width="90%"}
+knitr::include_graphics('images/p0000_2.png')
+```
+
+**2. Chinese version**
+
+- Episode 1: https://www.bilibili.com/video/BV1rT421k7Zv
+- Episode 2: https://www.bilibili.com/video/BV1E14218779
+- Episode 3: https://www.bilibili.com/video/BV141421t71g
+- Episode 4: https://www.bilibili.com/video/BV1TZ421K7VH
 
 ___