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Expand Up @@ -301,7 +301,7 @@ <h1 class="title">Orchestrating Hi-C analysis with Bioconductor</h1>


</header><p><img src="assets/cover.jpg" title="Orchestrating Hi-C analysis with Bioconductor" class="quarto-cover-image img-fluid"></p>
<p><strong>Package:</strong> OHCA<br><strong>Authors:</strong> Jacques Serizay [aut, cre]<br><strong>Compiled:</strong> 2023-11-07<br><strong>Package version:</strong> 0.98.1<br><strong>R version:</strong> <b style="color:red;">R Under development (unstable) (2023-11-02 r85465)</b><br><strong>BioC version:</strong> <b style="color:red;">3.19</b><br><strong>License:</strong> MIT + file LICENSE<br></p>
<p><strong>Package:</strong> OHCA<br><strong>Authors:</strong> Jacques Serizay [aut, cre]<br><strong>Compiled:</strong> 2023-11-07<br><strong>Package version:</strong> 0.99.0<br><strong>R version:</strong> <b style="color:red;">R Under development (unstable) (2023-11-02 r85465)</b><br><strong>BioC version:</strong> <b style="color:red;">3.19</b><br><strong>License:</strong> MIT + file LICENSE<br></p>
<section id="welcome" class="level1 unnumbered"><h1 class="unnumbered">Welcome</h1>
<p>This is the landing page of the <strong>“Orchestrating Hi-C analysis with Bioconductor”</strong> book. <strong>The primary aim of this book is to introduce the <code>R</code> user to Hi-C analysis</strong>. This book starts with key concepts important for the analysis of chromatin conformation capture and then presents <code>Bioconductor</code> tools that can be leveraged to process, analyze, explore and visualize Hi-C data.</p>
<section id="table-of-contents" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="table-of-contents">Table of contents</h2>
Expand Down Expand Up @@ -431,6 +431,7 @@ <h1 class="title">Orchestrating Hi-C analysis with Bioconductor</h1>
<section id="building-book" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="building-book">Building book</h2>
<p>The OHCA book has been rendered in R thanks to a number of packages, including but not only:</p>
<ul>
<li><strong><code>BiocBook</code></strong></li>
<li><code>devtools</code></li>
<li><code>quarto</code></li>
<li><code>rebook</code></li>
Expand Down Expand Up @@ -618,7 +619,6 @@ <h1 class="title">Orchestrating Hi-C analysis with Bioconductor</h1>
<span><span class="co">## HiContacts 1.5.0 2023-10-24 [2] Bioconductor</span></span>
<span><span class="co">## HiContactsData 1.5.0 2023-10-31 [2] Bioconductor</span></span>
<span><span class="co">## HiCool 1.3.0 2023-10-24 [2] Bioconductor</span></span>
<span><span class="co">## hicrep 1.12.2 2023-11-07 [2] Github (TaoYang-dev/hicrep@e485dfa)</span></span>
<span><span class="co">## highr 0.10 2022-12-22 [2] CRAN (R 4.4.0)</span></span>
<span><span class="co">## Hmisc 5.1-1 2023-09-12 [2] CRAN (R 4.4.0)</span></span>
<span><span class="co">## hms 1.1.3 2023-03-21 [2] CRAN (R 4.4.0)</span></span>
Expand Down Expand Up @@ -668,7 +668,7 @@ <h1 class="title">Orchestrating Hi-C analysis with Bioconductor</h1>
<span><span class="co">## munsell 0.5.0 2018-06-12 [2] CRAN (R 4.4.0)</span></span>
<span><span class="co">## nlme 3.1-163 2023-08-09 [3] CRAN (R 4.4.0)</span></span>
<span><span class="co">## nnet 7.3-19 2023-05-03 [3] CRAN (R 4.4.0)</span></span>
<span><span class="co">## OHCA 0.98.1 2023-11-07 [1] Bioconductor</span></span>
<span><span class="co">## OHCA 0.99.0 2023-11-07 [1] local</span></span>
<span><span class="co">## openssl 2.1.1 2023-09-25 [2] CRAN (R 4.4.0)</span></span>
<span><span class="co">## OrganismDbi 1.45.0 2023-10-25 [2] Bioconductor</span></span>
<span><span class="co">## packrat 0.9.2 2023-09-05 [2] CRAN (R 4.4.0)</span></span>
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<span><span class="co">## zip 2.3.0 2023-04-17 [2] CRAN (R 4.4.0)</span></span>
<span><span class="co">## zlibbioc 1.49.0 2023-10-24 [2] Bioconductor</span></span>
<span><span class="co">## </span></span>
<span><span class="co">## [1] /tmp/RtmpixmP1F/Rinst529f91dd</span></span>
<span><span class="co">## [1] /tmp/RtmpEEUcH8/Rinst555f2f89bc</span></span>
<span><span class="co">## [2] /usr/local/lib/R/site-library</span></span>
<span><span class="co">## [3] /usr/local/lib/R/library</span></span>
<span><span class="co">## </span></span>
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30 changes: 15 additions & 15 deletions docs/devel/pages/data-representation.html
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Expand Up @@ -1571,8 +1571,8 @@ <h1 class="title">
<p>This fetches files from the cloud, download them locally and returns the path of the local file.</p>
<div class="cell" data-layout-align="center">
<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">coolf</span></span>
<span><span class="co">## EH7702 </span></span>
<span><span class="co">## "/root/.cache/R/ExperimentHub/1701a09a86_7752"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span><span class="co">## EH7702 </span></span>
<span><span class="co">## "/root/.cache/R/ExperimentHub/174688ce76a_7752"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Similarly, example files are available for other file formats:</p>
<div class="cell" data-layout-align="center">
Expand Down Expand Up @@ -1642,15 +1642,15 @@ <h1 class="title">
<span><span class="co"># ----- This creates a connection to a `.(m)cool` file (path stored in `coolf`)</span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/CoolFile-class.html">CoolFile</a></span><span class="op">(</span><span class="va">coolf</span><span class="op">)</span></span>
<span><span class="co">## CoolFile object</span></span>
<span><span class="co">## .mcool file: /root/.cache/R/ExperimentHub/1701a09a86_7752 </span></span>
<span><span class="co">## .mcool file: /root/.cache/R/ExperimentHub/174688ce76a_7752 </span></span>
<span><span class="co">## resolution: 1000 </span></span>
<span><span class="co">## pairs file: </span></span>
<span><span class="co">## metadata(0):</span></span>
<span></span>
<span><span class="co"># ----- This creates a connection to a `.hic` file (path stored in `hicf`)</span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/HicFile-class.html">HicFile</a></span><span class="op">(</span><span class="va">hicf</span><span class="op">)</span></span>
<span><span class="co">## HicFile object</span></span>
<span><span class="co">## .hic file: /root/.cache/R/ExperimentHub/1702b65c0b7_7836 </span></span>
<span><span class="co">## .hic file: /root/.cache/R/ExperimentHub/17460f12195_7836 </span></span>
<span><span class="co">## resolution: 1000 </span></span>
<span><span class="co">## pairs file: </span></span>
<span><span class="co">## metadata(0):</span></span>
Expand All @@ -1659,16 +1659,16 @@ <h1 class="title">
<span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/HicproFile-class.html">HicproFile</a></span><span class="op">(</span><span class="va">hicpromatrixf</span>, <span class="va">hicproregionsf</span><span class="op">)</span></span>
<span><span class="co">## HicproFile object</span></span>
<span><span class="co">## HiC-Pro files:</span></span>
<span><span class="co">## $ matrix: /root/.cache/R/ExperimentHub/1707968a6f0_7837 </span></span>
<span><span class="co">## $ regions: /root/.cache/R/ExperimentHub/17073053091_7838 </span></span>
<span><span class="co">## $ matrix: /root/.cache/R/ExperimentHub/1745c1383e1_7837 </span></span>
<span><span class="co">## $ regions: /root/.cache/R/ExperimentHub/17439b9b892_7838 </span></span>
<span><span class="co">## resolution: 1000 </span></span>
<span><span class="co">## pairs file: </span></span>
<span><span class="co">## metadata(0):</span></span>
<span></span>
<span><span class="co"># ----- This creates a connection to a pairs file</span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/PairsFile-class.html">PairsFile</a></span><span class="op">(</span><span class="va">pairsf</span><span class="op">)</span></span>
<span><span class="co">## PairsFile object</span></span>
<span><span class="co">## resource: /root/.cache/R/ExperimentHub/1702dcdfa3b_7753</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span><span class="co">## resource: /root/.cache/R/ExperimentHub/174ff8a7b2_7753</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section><section id="contactfile-slots" class="level3" data-number="2.3.3"><h3 data-number="2.3.3" class="anchored" data-anchor-id="contactfile-slots">
<span class="header-section-number">2.3.3</span> <code>ContactFile</code> slots</h3>
Expand All @@ -1684,7 +1684,7 @@ <h1 class="title">
<div class="sourceCode" id="cb51"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">cf</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/CoolFile-class.html">CoolFile</a></span><span class="op">(</span><span class="va">coolf</span><span class="op">)</span></span>
<span><span class="va">cf</span></span>
<span><span class="co">## CoolFile object</span></span>
<span><span class="co">## .mcool file: /root/.cache/R/ExperimentHub/1701a09a86_7752 </span></span>
<span><span class="co">## .mcool file: /root/.cache/R/ExperimentHub/174688ce76a_7752 </span></span>
<span><span class="co">## resolution: 1000 </span></span>
<span><span class="co">## pairs file: </span></span>
<span><span class="co">## metadata(0):</span></span>
Expand Down Expand Up @@ -1782,7 +1782,7 @@ <h1 class="title">
<span><span class="va">hic</span></span>
<span><span class="co">## `HiCExperiment` object with 8,757,906 contacts over 12,079 regions </span></span>
<span><span class="co">## -------</span></span>
<span><span class="co">## fileName: "/root/.cache/R/ExperimentHub/1701a09a86_7752" </span></span>
<span><span class="co">## fileName: "/root/.cache/R/ExperimentHub/174688ce76a_7752" </span></span>
<span><span class="co">## focus: "whole genome" </span></span>
<span><span class="co">## resolutions(5): 1000 2000 4000 8000 16000</span></span>
<span><span class="co">## active resolution: 1000 </span></span>
Expand Down Expand Up @@ -1814,7 +1814,7 @@ <h1 class="title">
<p>These pieces of information are called <code>slots</code>. They can be directly accessed using <code>getter</code> functions, bearing the same name than the slot.</p>
<div class="cell" data-layout-align="center">
<div class="sourceCode" id="cb55"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/fileName.html">fileName</a></span><span class="op">(</span><span class="va">hic</span><span class="op">)</span></span>
<span><span class="co">## [1] "/root/.cache/R/ExperimentHub/1701a09a86_7752"</span></span>
<span><span class="co">## [1] "/root/.cache/R/ExperimentHub/174688ce76a_7752"</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/AllGenerics.html">focus</a></span><span class="op">(</span><span class="va">hic</span><span class="op">)</span></span>
<span><span class="co">## NULL</span></span>
Expand Down Expand Up @@ -1881,7 +1881,7 @@ <h1 class="title">
<span><span class="va">hic</span></span>
<span><span class="co">## `HiCExperiment` object with 13,681,280 contacts over 12,165 regions </span></span>
<span><span class="co">## -------</span></span>
<span><span class="co">## fileName: "/root/.cache/R/ExperimentHub/1702b65c0b7_7836" </span></span>
<span><span class="co">## fileName: "/root/.cache/R/ExperimentHub/17460f12195_7836" </span></span>
<span><span class="co">## focus: "whole genome" </span></span>
<span><span class="co">## resolutions(5): 1000 2000 4000 8000 16000</span></span>
<span><span class="co">## active resolution: 1000 </span></span>
Expand Down Expand Up @@ -2321,14 +2321,14 @@ <h1 class="title">
<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">yeast_hic</span></span>
<span><span class="co">## `HiCExperiment` object with 8,757,906 contacts over 763 regions </span></span>
<span><span class="co">## -------</span></span>
<span><span class="co">## fileName: "/root/.cache/R/ExperimentHub/1701a09a86_7752" </span></span>
<span><span class="co">## fileName: "/root/.cache/R/ExperimentHub/174688ce76a_7752" </span></span>
<span><span class="co">## focus: "whole genome" </span></span>
<span><span class="co">## resolutions(5): 1000 2000 4000 8000 16000</span></span>
<span><span class="co">## active resolution: 16000 </span></span>
<span><span class="co">## interactions: 267709 </span></span>
<span><span class="co">## scores(2): count balanced </span></span>
<span><span class="co">## topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) centromeres(16) </span></span>
<span><span class="co">## pairsFile: /root/.cache/R/ExperimentHub/1702dcdfa3b_7753 </span></span>
<span><span class="co">## pairsFile: /root/.cache/R/ExperimentHub/174ff8a7b2_7753 </span></span>
<span><span class="co">## metadata(3): ID org date</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<section id="interactions" class="level4" data-number="2.4.2.1"><h4 data-number="2.4.2.1" class="anchored" data-anchor-id="interactions">
Expand Down Expand Up @@ -2620,8 +2620,8 @@ <h1 class="title">
<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/AllGenerics.html">pairsFile</a></span><span class="op">(</span><span class="va">yeast_hic</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">pairsf</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/AllGenerics.html">pairsFile</a></span><span class="op">(</span><span class="va">yeast_hic</span><span class="op">)</span></span>
<span><span class="co">## EH7703 </span></span>
<span><span class="co">## "/root/.cache/R/ExperimentHub/1702dcdfa3b_7753"</span></span>
<span><span class="co">## EH7703 </span></span>
<span><span class="co">## "/root/.cache/R/ExperimentHub/174ff8a7b2_7753"</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/readLines.html">readLines</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/AllGenerics.html">pairsFile</a></span><span class="op">(</span><span class="va">yeast_hic</span><span class="op">)</span>, <span class="fl">25</span><span class="op">)</span></span>
<span><span class="co">## [1] "## pairs format v1.0" </span></span>
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