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disseminating.html

@@ -411,7 +411,7 @@ <h1 class="title">
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 <li>
-<code>type = 'insulation'</code> will fetch a <code>.bigwig</code> track file precomputed by the 4DN consortium. This track corresponds to the genome-wide insulation score computed by <code>cooltools</code> as described in <span class="citation" data-cites="Crane2015Jul">Crane et al. (<a href="interoperability.html#ref-Crane2015Jul" role="doc-biblioref">2015</a>)</span>. To know more about this, read <a href="https://data.4dnucleome.org/resources/data-analysis/insulation_compartment_scores#insulation_scores_and_boundaries_page_all">the excerpt from 4DN data portal</a>. Once fetched from the 4DN data portal, the local file can be imported in <code>R</code> using the <code>import</code> function, which will generate a <code>RleList</code> object.</li>
+<code>type = 'insulation'</code> will fetch a <code>.bigwig</code> track file precomputed by the 4DN consortium. This track corresponds to the genome-wide insulation score computed by <code>cooltools</code> as described in <span class="citation" data-cites="Crane_2015">Crane et al. (<a href="interoperability.html#ref-Crane_2015" role="doc-biblioref">2015</a>)</span>. To know more about this, read <a href="https://data.4dnucleome.org/resources/data-analysis/insulation_compartment_scores#insulation_scores_and_boundaries_page_all">the excerpt from 4DN data portal</a>. Once fetched from the 4DN data portal, the local file can be imported in <code>R</code> using the <code>import</code> function, which will generate a <code>RleList</code> object.</li>
 </ul>
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 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/fourDNData/man/fourDNData.html">fourDNData</a></span><span class="op">(</span>experimentSetAccession <span class="op">=</span> <span class="st">'4DNES25ABNZ1'</span>, type <span class="op">=</span> <span class="st">'insulation'</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
@@ -603,9 +603,9 @@ <h1 class="title">
 
 
 </section><section id="bibliography" class="level1 unnumbered"><h1 class="unnumbered">References</h1>
-<div id="refs" class="references csl-bib-body hanging-indent" role="list" style="display: none">
-<div id="ref-Crane2015Jul" class="csl-entry" role="listitem">
-Crane, Emily, Qian Bian, Rachel Patton McCord, Bryan R. Lajoie, Bayly S. Wheeler, Edward J. Ralston, Satoru Uzawa, Job Dekker, and Barbara J. Meyer. 2015. <span>“<span class="nocase">Condensin-driven remodelling of X chromosome topology during dosage compensation</span>.”</span> <em>Nature</em> 523 (July): 240–44. <a href="https://doi.org/10.1038/nature14450">https://doi.org/10.1038/nature14450</a>.
+<div id="refs" class="references csl-bib-body hanging-indent" data-line-spacing="2" role="list" style="display: none">
+<div id="ref-Crane_2015" class="csl-entry" role="listitem">
+Crane, E., Bian, Q., McCord, R. P., Lajoie, B. R., Wheeler, B. S., Ralston, E. J., Uzawa, S., Dekker, J., &amp; Meyer, B. J. (2015). Condensin-driven remodelling of x chromosome topology during dosage compensation. <em>Nature</em>, <em>523</em>(7559), 240–244. <a href="https://doi.org/10.1038/nature14450">https://doi.org/10.1038/nature14450</a>
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interactions-centric.html

@@ -372,7 +372,7 @@ <h1 class="title">
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">hic</span></span>
 <span><span class="co">##  `HiCExperiment` object with 471,364 contacts over 407 regions </span></span>
 <span><span class="co">##  -------</span></span>
-<span><span class="co">##  fileName: "/github/home/.cache/R/ExperimentHub/1a594277bd62_7752" </span></span>
+<span><span class="co">##  fileName: "/github/home/.cache/R/ExperimentHub/1a9a4dc30249_7752" </span></span>
 <span><span class="co">##  focus: "II" </span></span>
 <span><span class="co">##  resolutions(5): 1000 2000 4000 8000 16000</span></span>
 <span><span class="co">##  active resolution: 2000 </span></span>
@@ -400,7 +400,7 @@ <h1 class="title">
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 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">pf</span></span>
 <span><span class="co">##  PairsFile object</span></span>
-<span><span class="co">##  resource: /github/home/.cache/R/ExperimentHub/1a594e4de0cf_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: /github/home/.cache/R/ExperimentHub/1a9a1c034d7_7753</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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@@ -452,7 +452,7 @@ <h1 class="title">
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 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/js2264/HiContacts">HiContacts</a></span><span class="op">)</span></span>
 <span><span class="va">ps</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/HiContacts/man/Ps.html">distanceLaw</a></span><span class="op">(</span><span class="va">pf</span>, by_chr <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> </span>
-<span><span class="co">##  Importing pairs file /github/home/.cache/R/ExperimentHub/1a594e4de0cf_7753 in memory. This may take a while...</span></span>
+<span><span class="co">##  Importing pairs file /github/home/.cache/R/ExperimentHub/1a9a1c034d7_7753 in memory. This may take a while...</span></span>
 <span><span class="va">ps</span></span>
 <span><span class="co">##  # A tibble: 115 × 6</span></span>
 <span><span class="co">##    chr   binned_distance          p     norm_p norm_p_unity slope</span></span>
@@ -513,7 +513,7 @@ <h1 class="title">
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 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">eco1_ps</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/HiContacts/man/Ps.html">distanceLaw</a></span><span class="op">(</span><span class="va">eco1_pf</span>, by_chr <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> </span>
-<span><span class="co">##  Importing pairs file /github/home/.cache/R/ExperimentHub/21b95aa8e2b4_7755 in memory. This may take a while...</span></span>
+<span><span class="co">##  Importing pairs file /github/home/.cache/R/ExperimentHub/21fb251da216_7755 in memory. This may take a while...</span></span>
 <span><span class="va">eco1_ps</span></span>
 <span><span class="co">##  # A tibble: 115 × 6</span></span>
 <span><span class="co">##    chr   binned_distance          p     norm_p norm_p_unity slope</span></span>
@@ -694,12 +694,12 @@ <h1 class="title">
 <p>This clearly highlights trans interactions of the chromosome <code>II</code> centromere with the centromeres from other chromosomes.</p>
 </section><section id="scalograms" class="level2 page-columns page-full" data-number="6.4"><h2 data-number="6.4" class="anchored" data-anchor-id="scalograms">
 <span class="header-section-number">6.4</span> Scalograms</h2>
-<p>Scalograms were introduced in <span class="citation" data-cites="Lioy2018Feb">Lioy et al. (<a href="interoperability.html#ref-Lioy2018Feb" role="doc-biblioref">2018</a>)</span> to investigate distance-dependent contact frequencies for individual genomic bins along chromosomes.<br>
+<p>Scalograms were introduced in <span class="citation" data-cites="Lioy_2018">Lioy et al. (<a href="interoperability.html#ref-Lioy_2018" role="doc-biblioref">2018</a>)</span> to investigate distance-dependent contact frequencies for individual genomic bins along chromosomes.<br>
 To generate a scalogram, one needs to provide a <code>HiCExperiment</code> object with a valid associated <code>pairsFile</code>.</p>
 <div class="cell" data-layout-align="center" data-hash="interactions-centric_cache/html/unnamed-chunk-17_4e0d15336a002cea58219b80a7c4dc89">
 <div class="sourceCode" id="cb20"><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">hic</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">pairsf</span></span>
 <span><span class="va">scalo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/HiContacts/man/scalogram.html">scalogram</a></span><span class="op">(</span><span class="va">hic</span><span class="op">)</span> </span>
-<span><span class="co">##  Importing pairs file /github/home/.cache/R/ExperimentHub/1a594e4de0cf_7753 in memory. This may take a while...</span></span>
+<span><span class="co">##  Importing pairs file /github/home/.cache/R/ExperimentHub/1a9a1c034d7_7753 in memory. This may take a while...</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/HiContacts/man/plotScalogram.html">plotScalogram</a></span><span class="op">(</span><span class="va">scalo</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">chr</span> <span class="op">==</span> <span class="st">'II'</span><span class="op">)</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">1e3</span>, <span class="fl">1e5</span><span class="op">)</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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@@ -723,7 +723,7 @@ <h1 class="title">
 <span><span class="co">##  loading from cache</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">eco1_hic</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">eco1_pairsf</span></span>
 <span><span class="va">eco1_scalo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/HiContacts/man/scalogram.html">scalogram</a></span><span class="op">(</span><span class="va">eco1_hic</span><span class="op">)</span> </span>
-<span><span class="co">##  Importing pairs file /github/home/.cache/R/ExperimentHub/21b95aa8e2b4_7755 in memory. This may take a while...</span></span>
+<span><span class="co">##  Importing pairs file /github/home/.cache/R/ExperimentHub/21fb251da216_7755 in memory. This may take a while...</span></span>
 <span><span class="va">merged_scalo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/cbind.html">rbind</a></span><span class="op">(</span></span>
 <span>    <span class="va">scalo</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>sample <span class="op">=</span> <span class="st">'WT'</span><span class="op">)</span>, </span>
 <span>    <span class="va">eco1_scalo</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>sample <span class="op">=</span> <span class="st">'eco1'</span><span class="op">)</span></span>
@@ -742,9 +742,9 @@ <h1 class="title">
 
 
 </section><section id="bibliography" class="level1 unnumbered"><h1 class="unnumbered">References</h1>
-<div id="refs" class="references csl-bib-body hanging-indent" role="list" style="display: none">
-<div id="ref-Lioy2018Feb" class="csl-entry" role="listitem">
-Lioy, Virginia S., Axel Cournac, Martial Marbouty, Stéphane Duigou, Julien Mozziconacci, Olivier Espéli, Frédéric Boccard, and Romain Koszul. 2018. <span>“<span class="nocase">Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins</span>.”</span> <em>Cell</em> 172 (4): 771–78318. <a href="https://doi.org/10.1016/j.cell.2017.12.027">https://doi.org/10.1016/j.cell.2017.12.027</a>.
+<div id="refs" class="references csl-bib-body hanging-indent" data-line-spacing="2" role="list" style="display: none">
+<div id="ref-Lioy_2018" class="csl-entry" role="listitem">
+Lioy, V. S., Cournac, A., Marbouty, M., Duigou, S., Mozziconacci, J., Espéli, O., Boccard, F., &amp; Koszul, R. (2018). Multiscale structuring of the e.&nbsp;Coli chromosome by nucleoid-associated and condensin proteins. <em>Cell</em>, <em>172</em>(4), 771–783.e18. <a href="https://doi.org/10.1016/j.cell.2017.12.027">https://doi.org/10.1016/j.cell.2017.12.027</a>
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