render previous seven commits including cache

.quarto/crossref/index.qmd/index.html.json

@@ -1 +1 @@
-{"options":{"chapters":true},"headings":["preface"],"entries":[]}
+{"headings":["preface"],"entries":[],"options":{"chapters":true}}

.quarto/crossref/references.qmd/references.html.json

@@ -1 +1 @@
-{"options":{"chapters":true},"headings":[],"entries":[]}
+{"headings":[],"entries":[],"options":{"chapters":true}}

demo-genome-searching_cache/html/__packages

@@ -1,10 +1,3 @@
-base
-methods
-datasets
-utils
-grDevices
-graphics
-stats
 tidyverse
 ggplot2
 tibble

demo-phylogenetics_cache/html/__packages

@@ -0,0 +1,5 @@
+ggplot2
+dplyr
+stringr
+ape
+ggtree

docs/demo-genome-assembly.html

@@ -298,8 +298,7 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">15</span>&nb
     <h2 id="toc-title">Table of contents</h2>
 
   <ul>
-  <li><a href="#challenge" id="toc-challenge" class="nav-link active" data-scroll-target="#challenge">Challenge</a></li>
-  <li><a href="#download-the-reads" id="toc-download-the-reads" class="nav-link" data-scroll-target="#download-the-reads">Download the reads</a></li>
+  <li><a href="#download-the-reads" id="toc-download-the-reads" class="nav-link active" data-scroll-target="#download-the-reads">Download the reads</a></li>
   <li><a href="#assess-read-qualities" id="toc-assess-read-qualities" class="nav-link" data-scroll-target="#assess-read-qualities">Assess read qualities</a></li>
   <li><a href="#exploring-assemblers" id="toc-exploring-assemblers" class="nav-link" data-scroll-target="#exploring-assemblers">Exploring assemblers</a>
   <ul class="collapse">
@@ -334,11 +333,20 @@ <h1 class="title d-none d-lg-block"><span class="chapter-number">15</span>&nbsp;
 
 </header>
 
-<section id="challenge" class="level2 unnumbered">
-<h2 class="unnumbered anchored" data-anchor-id="challenge">Challenge</h2>
+<div class="callout-warning callout callout-style-default callout-captioned">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-caption-container flex-fill">
+Challenge
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <p>Your professor has sequenced a bacterial isolate using PacBio and Nanopore sequencing methods and has got the FASTQ files from both technologies. Now he needs to know the quality and quantity of these data before start any other analysis and ask you to assess the data. He needs to know how many sequences there are, how many base pairs (in GB) are there and the N50. He is also interested in see a visualization of the i) number of bases vs.&nbsp;sequence lengths (log transformed) and ii) the read length vs.&nbsp;read quality vs.&nbsp;read number.</p>
 <p>He ask you to document every step and to conclude what data should be used.</p>
-</section>
+</div>
+</div>
 <section id="download-the-reads" class="level2 unnumbered">
 <h2 class="unnumbered anchored" data-anchor-id="download-the-reads">Download the reads</h2>
 <div class="sourceCode" id="downloading-seqs"><pre class="sourceCode zsh important code-with-copy"><code class="sourceCode zsh"><span id="downloading-seqs-1"><a href="#downloading-seqs-1" aria-hidden="true" tabindex="-1"></a><span class="fu">wget</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

docs/demo-genome-searching.html

@@ -272,17 +272,12 @@ <h1 class="quarto-secondary-nav-title">
         <nav id="TOC" role="doc-toc"><h2 id="toc-title">Table of contents</h2>
 
   <ul>
-<li>
-<a href="#challenge" id="toc-challenge" class="nav-link active" data-scroll-target="#challenge">Challenge</a>
-  <ul class="collapse">
-<li><a href="#downloading-a-genome" id="toc-downloading-a-genome" class="nav-link" data-scroll-target="#downloading-a-genome">Downloading a genome</a></li>
+<li><a href="#downloading-a-genome" id="toc-downloading-a-genome" class="nav-link active" data-scroll-target="#downloading-a-genome">Downloading a genome</a></li>
   <li><a href="#downloading-from-ncbi" id="toc-downloading-from-ncbi" class="nav-link" data-scroll-target="#downloading-from-ncbi">Downloading from NCBI</a></li>
   <li><a href="#listing-files" id="toc-listing-files" class="nav-link" data-scroll-target="#listing-files">Listing files</a></li>
   <li><a href="#decompressing-using-gzip" id="toc-decompressing-using-gzip" class="nav-link" data-scroll-target="#decompressing-using-gzip">Decompressing using <code>gzip</code></a></li>
   <li><a href="#importing-the-files-into-r" id="toc-importing-the-files-into-r" class="nav-link" data-scroll-target="#importing-the-files-into-r">Importing the files into R</a></li>
   <li><a href="#data-processing" id="toc-data-processing" class="nav-link" data-scroll-target="#data-processing">Data processing</a></li>
-  </ul>
-</li>
   </ul><div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/camilogarciabotero/biocomp-book/edit/main/demo-genome-searching.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/camilogarciabotero/biocomp-book/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
     </div>
 <!-- main -->
@@ -307,8 +302,19 @@ <h1 class="title d-none d-lg-block">
   </div>
 
 
-</header><section id="challenge" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="challenge">Challenge</h2>
+</header><div class="callout-warning callout callout-style-default callout-captioned">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-caption-container flex-fill">
+Challenge
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <p>Your profesor is interested on knowing how many complete genomes of Bacillus subtilis are there in the NCBI databases. He ask you later to count the number of features (genes, CDS, ncRNA, rRNA, etc.) in the genome of Bacillus subtilis NCIB 3610 (GCF_002055965.1). And tell you to document each of the steps and how did you end up with the answer. Saving the file with your initials (e.g., CG-activity01.{md,txt,docx})</p>
+</div>
+</div>
 <section id="downloading-a-genome" class="level3 unnumbered"><h3 class="unnumbered anchored" data-anchor-id="downloading-a-genome">Downloading a genome</h3>
 <div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">ncbi-genome-download</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </section><section id="downloading-from-ncbi" class="level3 unnumbered"><h3 class="unnumbered anchored" data-anchor-id="downloading-from-ncbi">Downloading from NCBI</h3>
@@ -335,7 +341,7 @@ <h1 class="title d-none d-lg-block">
 </section>
 </div>
 </section><section id="importing-the-files-into-r" class="level3 unnumbered"><h3 class="unnumbered anchored" data-anchor-id="importing-the-files-into-r">Importing the files into R</h3>
-<div class="cell" data-warclass-warning="false" data-warattr-warning="false">
+<div class="cell" data-warclass-warning="false" data-warattr-warning="false" data-hash="demo-genome-searching_cache/html/file-reading_99207958b71348f644a376668f84e5aa">
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><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://tidyverse.tidyverse.org">tidyverse</a></span><span class="op">)</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://fs.r-lib.org">fs</a></span><span class="op">)</span>
 
@@ -375,7 +381,7 @@ <h1 class="title d-none d-lg-block">
 </div>
 </div>
 </section><section id="data-processing" class="level3 unnumbered"><h3 class="unnumbered anchored" data-anchor-id="data-processing">Data processing</h3>
-<div class="cell">
+<div class="cell" data-hash="demo-genome-searching_cache/html/data-processing_91bdbc4dd42bab566973aec10221dbcd">
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span class="va">all_features_grouped</span> <span class="op">&lt;-</span> <span class="va">all_features</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html">rename</a></span><span class="op">(</span>feature <span class="op">=</span> <span class="va">`# feature`</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">assembly</span>, <span class="va">feature</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html">%&gt;%</a></span> 
@@ -390,7 +396,7 @@ <h1 class="title d-none d-lg-block">
 <p>create a new dataset that will group by features per accession. get read of the weird name of the column. Select these two columns. Group by these two columns to perform. count the numbers of rows based on the applied group. generate a wide dataset sending row names as columns. Arrange descending by the number of CDSs.</p>
 
 
-</section></section></main><!-- /main --><script type="application/javascript">
+</section></main><!-- /main --><script type="application/javascript">
 window.document.addEventListener("DOMContentLoaded", function (event) {
   const disableStylesheet = (stylesheets) => {
     for (let i=0; i < stylesheets.length; i++) {

docs/demo-phylogenetics.html

@@ -272,8 +272,7 @@ <h1 class="quarto-secondary-nav-title">
         <nav id="TOC" role="doc-toc"><h2 id="toc-title">Table of contents</h2>
 
   <ul>
-<li><a href="#challenge" id="toc-challenge" class="nav-link active" data-scroll-target="#challenge">Challenge</a></li>
-  <li><a href="#sequence-alignment-cytb" id="toc-sequence-alignment-cytb" class="nav-link" data-scroll-target="#sequence-alignment-cytb">Sequence alignment <em>cytb</em></a></li>
+<li><a href="#sequence-alignment-cytb" id="toc-sequence-alignment-cytb" class="nav-link active" data-scroll-target="#sequence-alignment-cytb">Sequence alignment <em>cytb</em></a></li>
   <li><a href="#evolutionary-substitution-model" id="toc-evolutionary-substitution-model" class="nav-link" data-scroll-target="#evolutionary-substitution-model">Evolutionary substitution model</a></li>
   <li>
 <a href="#maximum-likelihood-reconstruction" id="toc-maximum-likelihood-reconstruction" class="nav-link" data-scroll-target="#maximum-likelihood-reconstruction">Maximum likelihood reconstruction</a>
@@ -311,9 +310,20 @@ <h1 class="title d-none d-lg-block">
   </div>
 
 
-</header><section id="challenge" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="challenge">Challenge</h2>
+</header><div class="callout-warning callout callout-style-default callout-captioned">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-caption-container flex-fill">
+Challenge
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <p>Your professor has been working with some mammal species and want to know the relationships of some sampled individuals. To do so he extracted the DNA and amplified the mitochondrial CYTB gene of those individuals. He gives a folder with multiple sequences and ask you to align them and to reconstruct two trees one using maximum likelihood (ML) and other using a Bayesian inference (BI). Then ask you to explain if both trees are congruent with each other.</p>
-</section><section id="sequence-alignment-cytb" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="sequence-alignment-cytb">Sequence alignment <em>cytb</em>
+</div>
+</div>
+<section id="sequence-alignment-cytb" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="sequence-alignment-cytb">Sequence alignment <em>cytb</em>
 </h2>
 <div class="sourceCode" id="cb1"><pre class="sourceCode zsh code-with-copy"><code class="sourceCode zsh"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">linsi</span> <span class="at">--preservecase</span> <span class="at">--reorder</span> cytB.fasta <span class="op">&gt;</span> cytB-aligned.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </section><section id="evolutionary-substitution-model" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="evolutionary-substitution-model">Evolutionary substitution model</h2>
@@ -322,10 +332,10 @@ <h1 class="title d-none d-lg-block">
 </section><section id="maximum-likelihood-reconstruction" class="level2 unnumbered"><h2 class="unnumbered anchored" data-anchor-id="maximum-likelihood-reconstruction">Maximum likelihood reconstruction</h2>
 <div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">raxml-ng</span> <span class="at">--msa</span> cytB-aligned.fasta <span class="at">--model</span> GTR+I+G4</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <section id="tree-building" class="level3 unnumbered"><h3 class="unnumbered anchored" data-anchor-id="tree-building">Tree building</h3>
-<div class="cell">
+<div class="cell" data-hash="demo-phylogenetics_cache/html/unnamed-chunk-1_5f67f100fe84738a6334ee503853aa01">
 
 </div>
-<div class="cell" data-layout-align="center">
+<div class="cell" data-layout-align="center" data-hash="demo-phylogenetics_cache/html/unnamed-chunk-2_9a8627b847bc61523d91927402fcd53d">
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span class="va">raxml_data</span> <span class="op">&lt;-</span> <span class="fu">read.tree</span><span class="op">(</span><span class="st">"cytB-aligned.fasta.raxml.support"</span><span class="op">)</span>
 
 <span class="va">raxml_data</span><span class="op">$</span><span class="va">tip.label</span> <span class="op">&lt;-</span> <span class="fu">str_replace_all</span><span class="op">(</span><span class="va">raxml_data</span><span class="op">$</span><span class="va">tip.label</span>, <span class="st">"_"</span>, <span class="st">" "</span><span class="op">)</span>

docs/demo-reads-assessment.html

@@ -298,8 +298,7 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">14</span>&nb
     <h2 id="toc-title">Table of contents</h2>
 
   <ul>
-  <li><a href="#challenge" id="toc-challenge" class="nav-link active" data-scroll-target="#challenge">Challenge</a></li>
-  <li><a href="#general-stats-from-fastq-files" id="toc-general-stats-from-fastq-files" class="nav-link" data-scroll-target="#general-stats-from-fastq-files">General stats from fastq files</a></li>
+  <li><a href="#general-stats-from-fastq-files" id="toc-general-stats-from-fastq-files" class="nav-link active" data-scroll-target="#general-stats-from-fastq-files">General stats from fastq files</a></li>
   <li><a href="#a-graphical-assessment-of-reads" id="toc-a-graphical-assessment-of-reads" class="nav-link" data-scroll-target="#a-graphical-assessment-of-reads">A graphical assessment of reads</a></li>
   </ul>
 <div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/camilogarciabotero/biocomp-book/edit/main/demo-reads-assessment.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/camilogarciabotero/biocomp-book/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
@@ -329,10 +328,19 @@ <h1 class="title d-none d-lg-block"><span class="chapter-number">14</span>&nbsp;
 
 </header>
 
-<section id="challenge" class="level2 unnumbered">
-<h2 class="unnumbered anchored" data-anchor-id="challenge">Challenge</h2>
+<div class="callout-warning callout callout-style-default callout-captioned">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-caption-container flex-fill">
+Challenge
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <p>Your professor challenges you to assembly a bacterial genome. He wants to know if an assembly using Illumina reads or Nanopore reads is better. The raw sequences for Illumina could be downloaded with the code SRR15634574. And the Nanopore raw reads with SRR15634573 here: https://sra-explorer.info. Choose at least on set and follow the instruction from the lecture to assemble the genome. Document each step and send to the professor the <code>assembly-{your-initials}.fasta</code>. You could form groups of max. 4 students.</p>
-</section>
+</div>
+</div>
 <section id="general-stats-from-fastq-files" class="level2 unnumbered">
 <h2 class="unnumbered anchored" data-anchor-id="general-stats-from-fastq-files">General stats from fastq files</h2>
 <p>A simple but fast cli to display the general stats from fastq is <code>seqfu</code></p>