Skip to content

Commit

Permalink
Deploying to gh-pages from @ e53fd0b 🚀
Browse files Browse the repository at this point in the history
  • Loading branch information
js2264 committed Aug 8, 2023
1 parent 73aea99 commit eb1a1d9
Show file tree
Hide file tree
Showing 7 changed files with 93 additions and 21 deletions.
21 changes: 16 additions & 5 deletions docs/devel/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -109,10 +109,6 @@
"search-label": "Search"
}
}</script>
<meta property="og:title" content="Writing reproducible books with Bioconductor">
<meta property="og:description" content="">
<meta property="og:image" content="inst/assets/cover.png">
<meta property="og:site-name" content="Writing reproducible books with Bioconductor">
</head>
<body class="nav-sidebar docked slimcontent">

Expand Down Expand Up @@ -147,6 +143,21 @@
Browse version `devel`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.17/">
Browse version `3.17`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.16/">
Browse version `3.16`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.15/">
Browse version `3.15`
</a>
</li>
</ul>
</div>
</div>
Expand Down Expand Up @@ -230,7 +241,7 @@ <h1 class="title">Writing reproducible books with Bioconductor</h1>
<p><strong>Package:</strong> BiocBook<br><strong>Authors:</strong> First Last [aut, cre]<br><strong>Version:</strong> 0.99.0<br><strong>Modified:</strong> 2023-08-03<br><strong>Compiled:</strong> 2023-08-08<br><strong>Environment:</strong> R version 4.3.1 (2023-06-16), Bioconductor 3.18<br><strong>License:</strong> MIT + file LICENSE<br><strong>Copyright:</strong> Bioconductor, 2023</p>
<p>This is the landing page of the <code>BiocBook</code> entitled <em>Write, containerize, publish and versionize Quarto books with Bioconductor</em>.</p>
<p>This book introduces the reader to the <code>BiocBook</code> <strong>package</strong> and the auto-generated, versionized <strong>Docker images</strong> and <strong>website</strong>.</p>
<p><img src="../inst/img/workflow.png" class="img-fluid" style="width:50.0%"></p>
<p><img src="../inst/img/workflow.png" class="img-fluid"></p>
</section><section id="docker-image" class="level1 unnumbered"><h1 class="unnumbered">Docker image</h1>
<p>A <code>Docker</code> image built from this repository is available here:</p>
<p>👉 <a href="https://ghcr.io/js2264/biocbook">ghcr.io/js2264/biocbook</a> 🐳</p>
Expand Down
18 changes: 15 additions & 3 deletions docs/devel/pages/Chapter-1.html
Original file line number Diff line number Diff line change
Expand Up @@ -110,9 +110,6 @@
"search-label": "Search"
}
}</script>
<meta property="og:title" content="Writing reproducible books with Bioconductor - 1&nbsp; Write a BiocBook package">
<meta property="og:description" content="">
<meta property="og:site-name" content="Writing reproducible books with Bioconductor">
</head>
<body class="nav-sidebar docked slimcontent">

Expand Down Expand Up @@ -147,6 +144,21 @@
Browse version `devel`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.17/">
Browse version `3.17`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.16/">
Browse version `3.16`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.15/">
Browse version `3.15`
</a>
</li>
</ul>
</div>
</div>
Expand Down
17 changes: 15 additions & 2 deletions docs/devel/pages/Chapter-2.html
Original file line number Diff line number Diff line change
Expand Up @@ -64,8 +64,6 @@
}</script>


<meta property="og:title" content="Writing reproducible books with Bioconductor - 2&nbsp; Containerize a BiocBook package into a Docker image">
<meta property="og:site-name" content="Writing reproducible books with Bioconductor">
</head>

<body class="nav-sidebar docked">
Expand Down Expand Up @@ -107,6 +105,21 @@
Browse version `devel`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.17/">
Browse version `3.17`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.16/">
Browse version `3.16`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.15/">
Browse version `3.15`
</a>
</li>
</ul>
</div>
</div>
Expand Down
17 changes: 15 additions & 2 deletions docs/devel/pages/Chapter-3.html
Original file line number Diff line number Diff line change
Expand Up @@ -64,8 +64,6 @@
}</script>


<meta property="og:title" content="Writing reproducible books with Bioconductor - 3&nbsp; Publish a BiocBook package as a website">
<meta property="og:site-name" content="Writing reproducible books with Bioconductor">
</head>

<body class="nav-sidebar docked">
Expand Down Expand Up @@ -107,6 +105,21 @@
Browse version `devel`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.17/">
Browse version `3.17`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.16/">
Browse version `3.16`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.15/">
Browse version `3.15`
</a>
</li>
</ul>
</div>
</div>
Expand Down
18 changes: 15 additions & 3 deletions docs/devel/pages/Chapter-4.html
Original file line number Diff line number Diff line change
Expand Up @@ -90,9 +90,6 @@
"search-label": "Search"
}
}</script>
<meta property="og:title" content="Writing reproducible books with Bioconductor - 4&nbsp; Containerize and Publish against specific Bioconductor release versions">
<meta property="og:description" content="">
<meta property="og:site-name" content="Writing reproducible books with Bioconductor">
</head>
<body class="nav-sidebar docked">

Expand Down Expand Up @@ -127,6 +124,21 @@
Browse version `devel`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.17/">
Browse version `3.17`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.16/">
Browse version `3.16`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.15/">
Browse version `3.15`
</a>
</li>
</ul>
</div>
</div>
Expand Down
21 changes: 16 additions & 5 deletions docs/devel/pages/preamble.html
Original file line number Diff line number Diff line change
Expand Up @@ -91,10 +91,6 @@
"search-label": "Search"
}
}</script>
<meta property="og:title" content="Writing reproducible books with Bioconductor - Preamble">
<meta property="og:description" content="">
<meta property="og:image" content="../inst/img/workflow.png">
<meta property="og:site-name" content="Writing reproducible books with Bioconductor">
</head>
<body class="nav-sidebar docked">

Expand Down Expand Up @@ -129,6 +125,21 @@
Browse version `devel`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.17/">
Browse version `3.17`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.16/">
Browse version `3.16`
</a>
</li>
<li>
<a class="dropdown-item sidebar-tools-main-item" href="https://js2264.github.io/BiocBook/3.15/">
Browse version `3.15`
</a>
</li>
</ul>
</div>
</div>
Expand Down Expand Up @@ -330,7 +341,7 @@ <h1 class="title">Preamble</h1>
</div>
</section><section id="so-what-packages-can-i-use" class="level2"><h2 class="anchored" data-anchor-id="so-what-packages-can-i-use">So what packages can I use?</h2>
<p>Any package that has been released in the Bioconductor version you are using (in this book version, this is 3.18).</p>
<p>The <code>HiContacts</code> package is available in Bioconductor since <code>3.16</code>, while the <code>HiCExperiment</code> package was only made available in <code>3.17</code>. <code>MICSQTL</code> has recently been accepted in <code>3.18</code> (current <code>devel</code>, on Tue Aug 8 08:51:28 2023). Let’s check this!</p>
<p>The <code>HiContacts</code> package is available in Bioconductor since <code>3.16</code>, while the <code>HiCExperiment</code> package was only made available in <code>3.17</code>. <code>MICSQTL</code> has recently been accepted in <code>3.18</code> (current <code>devel</code>, on Tue Aug 8 09:08:33 2023). Let’s check this!</p>
<div class="cell" data-layout-align="center">
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://bioconductor.github.io/BiocManager/reference/available.html">available</a></span><span class="op">(</span><span class="st">"HiContacts"</span><span class="op">)</span></span>
<span><span class="co">## 'getOption("repos")' replaces Bioconductor standard repositories, see</span></span>
Expand Down
2 changes: 1 addition & 1 deletion docs/devel/search.json
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@
"href": "pages/preamble.html#so-what-packages-can-i-use",
"title": "Preamble",
"section": "So what packages can I use?",
"text": "So what packages can I use?\nAny package that has been released in the Bioconductor version you are using (in this book version, this is 3.18).\nThe HiContacts package is available in Bioconductor since 3.16, while the HiCExperiment package was only made available in 3.17. MICSQTL has recently been accepted in 3.18 (current devel, on Tue Aug 8 08:51:28 2023). Let’s check this!\n\nBiocManager::available(\"HiContacts\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"HiContacts\" \"HiContactsData\"\nBiocManager::available(\"HiCExperiment\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"HiCExperiment\"\nBiocManager::available(\"MICSQTL\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"MICSQTL\""
"text": "So what packages can I use?\nAny package that has been released in the Bioconductor version you are using (in this book version, this is 3.18).\nThe HiContacts package is available in Bioconductor since 3.16, while the HiCExperiment package was only made available in 3.17. MICSQTL has recently been accepted in 3.18 (current devel, on Tue Aug 8 09:08:33 2023). Let’s check this!\n\nBiocManager::available(\"HiContacts\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"HiContacts\" \"HiContactsData\"\nBiocManager::available(\"HiCExperiment\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"HiCExperiment\"\nBiocManager::available(\"MICSQTL\")\n## 'getOption(\"repos\")' replaces Bioconductor standard repositories, see\n## 'help(\"repositories\", package = \"BiocManager\")' for details.\n## Replacement repositories:\n## CRAN: https://cloud.r-project.org\n## [1] \"MICSQTL\""
},
{
"objectID": "pages/Chapter-1.html#register-a-github-account-in-r",
Expand Down

0 comments on commit eb1a1d9

Please sign in to comment.