rebuild book

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docs/sec-design.html

@@ -13,7 +13,7 @@
 
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docs/sec-git.html

@@ -13,7 +13,7 @@
 
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@@ -285,8 +285,8 @@ <h3>Track changes<div class="tooltip"><button class="internal-link-btn" onclick=
 a user is connected to an on-line version of the editor (such as
 Google docs or Microsoft Office 365).</li>
 <li>Once a track change is accepted or rejected, it isn’t possible to
-return to previous version. Google docs’ version history does allow
-this.</li>
+return to previous version. Google and Microsoft OneDrive documents
+do allow this.</li>
 <li>Track changes are only applicable to their respective formats, and
 not to code files, Rmd documents, or other text-based files.</li>
 <li>Track changes work on a single file, while version control records
@@ -306,11 +306,10 @@ <h2>
 <span class="header-section-number">11.3</span> Introduction to Git and GitHub<div class="tooltip"><button class="internal-link-btn" onclick="copy_link('introduction-to-git-and-github')" onmouseout="reset_tooltip('introduction-to-git-and-github-tooltip')"><span class="tooltiptext" id="introduction-to-git-and-github-tooltip">Copy link</span><i class="fa fa-link"></i></button></div>
 </h2>
 <p>Git is the automated version control software that we will be
-using. GitHub is an web interface to Git that allows to share a
-version control project over the internet, facilitates some operations
-to work collaboratively on-line and enables discussions
-(i.e. issues). Let’s start by explaining some fundamental Git
-concepts.</p>
+using. GitHub is a web interface to Git that allows to share a version
+control project over the internet, facilitates some operations to work
+collaboratively on-line and enables discussions (i.e. issues). Let’s
+start by explaining some fundamental Git concepts.</p>
 <div id="git" class="section level3 unnumbered">
 <h3>Git<div class="tooltip"><button class="internal-link-btn" onclick="copy_link('git')" onmouseout="reset_tooltip('git-tooltip')"><span class="tooltiptext" id="git-tooltip">Copy link</span><i class="fa fa-link"></i></button></div>
 </h3>
@@ -344,10 +343,10 @@ <h3>Git<div class="tooltip"><button class="internal-link-btn" onclick="copy_link
 <em>changeset</em>. All these files can now be effectively <em>committed</em>,
 i.e. that all the changes, who made them, and when they were added,
 are recorded and added to the version control.</p>
-<p>Note that Git doesn’t not record the complete file at each
-modification, but only the differences between each file. Knowing the
-difference between the current and previous states of a file is enough
-to reconstruct the previous version(s).</p>
+<p>Note that Git does not record the complete file at each modification,
+but only the differences between each file. Knowing the difference
+between the current and previous states of a file is enough to
+reconstruct the previous version(s).</p>
 <div class="figure" style="text-align: center">
 <span style="display:block;" id="fig:git2"></span>
 <p class="caption marginnote shownote">
@@ -429,8 +428,10 @@ <h3>GitHub<div class="tooltip"><button class="internal-link-btn" onclick="copy_l
 conflicting modifications:</li>
 </ul>
 <pre><code>Alice and Bastien</code></pre>
-<p>and then push again.
-- Alice can not pull to retrieve Bastien’s changes from the remote.</p>
+<p>and then push again.</p>
+<ul>
+<li>Alice can not pull to retrieve Bastien’s changes from the remote.</li>
+</ul>
 </div>
 </div>
 <div id="getting-started" class="section level2" number="11.4">
@@ -533,7 +534,7 @@ <h3>
 user, along with the authorization the user has. You can thus NOT use
 your GitHub password as a way to connect to your repository using
 RStudio.</p>
-<p>A PAT can be created on GitHub, in <em>settings &gt; Developer Settings &gt;
+<p>A PAT can be created on GitHub, in <em>Settings &gt; Developer Settings &gt;
 Personal</em> <em>access tokens &gt; Tokens (classic)</em> or directly
 <a href="https://github.com/settings/tokens">here</a>. Click on <em>Generate token
 (classic)</em> and configure you’re token. You can configure :</p>
@@ -681,16 +682,23 @@ <h2>
 <ul>
 <li>The easiest way to avoid conflicts is to always be in sync with the
 remote repository. To do so, always pull the latest changes before
-starting to work on a project.</li>
+starting to work on a project, and regularly push so that you
+co-workers can also stay in sync with your changes.</li>
 </ul>
 <p>To further avoid conflicts, try to modularise your project by
 splitting the work into multiple independent files. For an Rmd
-project:
-- the code for new sections could initially be written in separate
+project:</p>
+<ul>
+<li>the code for new sections could initially be written in separate
 code files so as to avoid breaking the compilation of the Rmd file
-when developing the new analysis;
-- save intermediate data and results so that others can re-use them
-independently of the whole pipeline.</p>
+when developing the new analysis;</li>
+<li>save intermediate data and results so that others can re-use them
+independently of the whole pipeline;</li>
+<li>given that Git compares documents line by line to assess if it can
+merge them automatically, use shorter lines (i.e. split your
+sentences and paragraphes over more lines) to reduce the risk of
+conflicts.</li>
+</ul>
 <p>GitHub issues are a useful way to discuss any specific points and
 centralise coordination in a project.</p>
 <p>It is possible to cancel commit if you forgot to pull before working
@@ -810,7 +818,7 @@ <h3>
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 </p>
 <p class="build-date">Page built: 
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+2024-10-31
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docs/sec-gsea.html

@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-10-30" />
+<meta name="date" content="2024-10-31" />
 
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@@ -711,10 +711,10 @@ <h2>
 ##         &lt;character&gt; &lt;character&gt;  &lt;factor&gt;  &lt;numeric&gt;
 ## sample1       Cell1  Epithelial      KD     0.726883
 ## sample2       Cell1  Epithelial      KD     1.308664
-## sample3       Cell1  Epithelial      mock   1.077368
+## sample3       Cell1  Epithelial      KD     1.077368
 ## sample4       Cell1  Epithelial      mock   0.966025
 ## sample5       Cell1  Epithelial      mock   1.042111
-## sample6       Cell1  Epithelial      KD     1.012664</code></pre>
+## sample6       Cell1  Epithelial      mock   1.012664</code></pre>
 <div class="sourceCode" id="cb292"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb292-1"><a href="sec-gsea.html#cb292-1" tabindex="-1"></a>ensembl_to_geneName <span class="ot">&lt;-</span> <span class="fu">tibble</span>(<span class="at">ENSEMBL =</span> <span class="fu">rownames</span>(dds)) <span class="sc">%&gt;%</span></span>
 <span id="cb292-2"><a href="sec-gsea.html#cb292-2" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">gene =</span> AnnotationDbi<span class="sc">::</span><span class="fu">mapIds</span>(org.Hs.eg.db, ENSEMBL, <span class="st">"SYMBOL"</span>,</span>
 <span id="cb292-3"><a href="sec-gsea.html#cb292-3" tabindex="-1"></a>                                      <span class="st">"ENSEMBL"</span>)) <span class="sc">%&gt;%</span></span>
@@ -737,22 +737,22 @@ <h2>
 <span id="cb292-20"><a href="sec-gsea.html#cb292-20" tabindex="-1"></a>    <span class="fu">mutate</span>(<span class="at">score =</span> <span class="fu">cumsum</span>(score))</span>
 <span id="cb292-21"><a href="sec-gsea.html#cb292-21" tabindex="-1"></a></span>
 <span id="cb292-22"><a href="sec-gsea.html#cb292-22" tabindex="-1"></a>res_tmp</span></code></pre></div>
-<pre><code>## # A tibble: 22,224 × 5
-##    ENSEMBL         ENTREZID   padj inGO  score
-##    &lt;chr&gt;           &lt;chr&gt;     &lt;dbl&gt; &lt;lgl&gt; &lt;dbl&gt;
-##  1 ENSG00000278267 102466751 0.998 FALSE    -1
-##  2 ENSG00000233750 100420257 0.998 FALSE    -2
-##  3 ENSG00000228463 728481    0.998 FALSE    -3
-##  4 ENSG00000236679 728517    0.998 FALSE    -4
-##  5 ENSG00000225972 100887749 0.998 FALSE    -5
-##  6 ENSG00000225630 100652939 0.998 FALSE    -6
-##  7 ENSG00000237973 107075141 0.998 FALSE    -7
-##  8 ENSG00000229344 107075310 0.998 FALSE    -8
-##  9 ENSG00000248527 106480796 0.998 FALSE    -9
-## 10 ENSG00000198744 107075270 0.998 FALSE   -10
-## # ℹ 22,214 more rows</code></pre>
+<pre><code>## # A tibble: 14,012 × 5
+##    ENSEMBL         ENTREZID      padj inGO  score
+##    &lt;chr&gt;           &lt;chr&gt;        &lt;dbl&gt; &lt;lgl&gt; &lt;dbl&gt;
+##  1 ENSG00000101856 10857    1.36e-147 FALSE  -1  
+##  2 ENSG00000177494 79413    5.17e- 67 FALSE  -2  
+##  3 ENSG00000136159 55270    1.83e- 44 FALSE  -3  
+##  4 ENSG00000175315 1474     9.11e- 43 FALSE  -4  
+##  5 ENSG00000128245 7533     1.87e- 42 FALSE  -5  
+##  6 ENSG00000113272 54974    9.51e- 39 FALSE  -6  
+##  7 ENSG00000213853 2013     2.00e- 36 FALSE  -7  
+##  8 ENSG00000115107 55240    1.48e- 33 FALSE  -8  
+##  9 ENSG00000008513 6482     1.17e- 32 FALSE  -9  
+## 10 ENSG00000105855 3696     3.75e- 31 TRUE   28.1
+## # ℹ 14,002 more rows</code></pre>
 <div class="sourceCode" id="cb294"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb294-1"><a href="sec-gsea.html#cb294-1" tabindex="-1"></a><span class="fu">max</span>(res_tmp<span class="sc">$</span>score)</span></code></pre></div>
-<pre><code>## [1] 394.1317</code></pre>
+<pre><code>## [1] 2155.674</code></pre>
 <div class="sourceCode" id="cb296"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb296-1"><a href="sec-gsea.html#cb296-1" tabindex="-1"></a><span class="fu">plot</span>(res_tmp<span class="sc">$</span>score, <span class="at">type =</span> <span class="st">"l"</span>)</span></code></pre></div>
 <p><img src="WSBIM2122_files/figure-html/gsea_res-1.png" width="672"></p>
 <p>This approach is very time consuming, given that the statistical tests
@@ -1267,7 +1267,7 @@ <h2>
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docs/sec-hts.html

@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-10-30" />
+<meta name="date" content="2024-10-31" />
 
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@@ -706,8 +706,8 @@ <h2>
 the raw counts of each gene in that sample.</p>
 <div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb92-1"><a href="sec-hts.html#cb92-1" tabindex="-1"></a>counts_result <span class="ot">&lt;-</span> <span class="fu">read_tsv</span>(<span class="at">file =</span> <span class="st">"wsbim2122_data/count_data/sample1_counts.tsv.gz"</span>)</span>
 <span id="cb92-2"><a href="sec-hts.html#cb92-2" tabindex="-1"></a><span class="fu">datatable</span>(<span class="fu">head</span>(counts_result))</span></code></pre></div>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-29364df67c4f3cfb87ef" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-29364df67c4f3cfb87ef">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5","6"],["ENSG00000223972","ENSG00000227232","ENSG00000278267","ENSG00000243485","ENSG00000284332","ENSG00000237613"],["1;1;1;1;1;1;1;1;1","1;1;1;1;1;1;1;1;1;1;1","1","1;1;1;1;1","1","1;1;1;1;1"],["11869;12010;12179;12613;12613;12975;13221;13221;13453","14404;15005;15796;16607;16858;17233;17606;17915;18268;24738;29534","17369","29554;30267;30564;30976;30976","30366","34554;35245;35277;35721;35721"],["12227;12057;12227;12721;12697;13052;13374;14409;13670","14501;15038;15947;16765;17055;17368;17742;18061;18366;24891;29570","17436","30039;30667;30667;31109;31097","30503","35174;35481;35481;36073;36081"],["+;+;+;+;+;+;+;+;+","-;-;-;-;-;-;-;-;-;-;-","-","+;+;+;+;+","+","-;-;-;-;-"],[1735,1351,68,1021,138,1219],[0,14,8,0,0,0]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Geneid<\/th>\n      <th>Chr<\/th>\n      <th>Start<\/th>\n      <th>End<\/th>\n      <th>Strand<\/th>\n      <th>Length<\/th>\n      <th>../processed_data/bam/sample1.bam<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[6,7]},{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Geneid","targets":1},{"name":"Chr","targets":2},{"name":"Start","targets":3},{"name":"End","targets":4},{"name":"Strand","targets":5},{"name":"Length","targets":6},{"name":"../processed_data/bam/sample1.bam","targets":7}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script><div class="question">
+<div class="datatables html-widget html-fill-item" id="htmlwidget-4a0a030fe545457a911a" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-4a0a030fe545457a911a">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5","6"],["ENSG00000223972","ENSG00000227232","ENSG00000278267","ENSG00000243485","ENSG00000284332","ENSG00000237613"],["1;1;1;1;1;1;1;1;1","1;1;1;1;1;1;1;1;1;1;1","1","1;1;1;1;1","1","1;1;1;1;1"],["11869;12010;12179;12613;12613;12975;13221;13221;13453","14404;15005;15796;16607;16858;17233;17606;17915;18268;24738;29534","17369","29554;30267;30564;30976;30976","30366","34554;35245;35277;35721;35721"],["12227;12057;12227;12721;12697;13052;13374;14409;13670","14501;15038;15947;16765;17055;17368;17742;18061;18366;24891;29570","17436","30039;30667;30667;31109;31097","30503","35174;35481;35481;36073;36081"],["+;+;+;+;+;+;+;+;+","-;-;-;-;-;-;-;-;-;-;-","-","+;+;+;+;+","+","-;-;-;-;-"],[1735,1351,68,1021,138,1219],[0,14,8,0,0,0]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Geneid<\/th>\n      <th>Chr<\/th>\n      <th>Start<\/th>\n      <th>End<\/th>\n      <th>Strand<\/th>\n      <th>Length<\/th>\n      <th>../processed_data/bam/sample1.bam<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[6,7]},{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Geneid","targets":1},{"name":"Chr","targets":2},{"name":"Start","targets":3},{"name":"End","targets":4},{"name":"Strand","targets":5},{"name":"Length","targets":6},{"name":"../processed_data/bam/sample1.bam","targets":7}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script><div class="question">
 <p class="question-begin">
 ► Question
 </p>
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@@ -13,7 +13,7 @@
 
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