Deploying to gh-pages from @ lmweber/BestPracticesST@e44e3c2 🚀

docs/devel/index.html

@@ -344,8 +344,8 @@ <h1 class="title">BestPracticesST</h1>
 <p><strong>Published:</strong> September 26, 2024<br></p>
 <section id="welcome" class="level1 unnumbered"><h1 class="unnumbered">Welcome</h1>
 <p>This is the website for the online book <strong>‘Best Practices for Spatial Transcriptomics Analysis with Bioconductor’</strong>.</p>
-<p>This book provides discussion and interactive examples on best practices for computational analysis workflows for spatial transcriptomics data, using the <a href="http://bioconductor.org/">Bioconductor</a> framework within R. The chapters contain details on individual analysis steps as well as complete example workflows, with interactive example datasets and R code.</p>
-<p>The book is organized into several parts, including introductory materials, analysis steps, and example workflows, for sequencing-based and imaging-based spatial transcriptomics platforms.</p>
+<p>This book provides discussion and interactive examples on best practices for computational analysis workflows for spatial transcriptomics data, using <a href="http://bioconductor.org/">Bioconductor</a> in R. The chapters contain details on individual analysis steps and longer workflows, with interactive examples consisting of R code and example datasets.</p>
+<p>The book is organized into several parts, including introductory materials, analysis steps, and longer workflows, for sequencing-based and imaging-based spatial transcriptomics platforms.</p>
 <p>Additional details on analysis workflows for non-spatial single-cell data as well as further introductory materials on R and Bioconductor can be found in the related book <a href="https://bioconductor.org/books/release/OSCA/">Orchestrating Single-Cell Analysis with Bioconductor (OSCA)</a>.</p>
 
 

docs/devel/pages/feature-selection.html

@@ -515,7 +515,7 @@ <h1 class="title"><span id="sec-feature-selection" class="quarto-section-identif
 <span><span class="co">##  ENSG00000162545 ENSG00000162545     CAMK2N1 Gene Expression        FALSE</span></span>
 <span><span class="co">##                    sigma.sq    tau.sq       phi    loglik   runtime      mean</span></span>
 <span><span class="co">##                   &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt;</span></span>
-<span><span class="co">##  ENSG00000074800 0.00840777  0.518011  15.82454  -109.808     0.016   1.75820</span></span>
+<span><span class="co">##  ENSG00000074800 0.00840777  0.518011  15.82454  -109.808     0.015   1.75820</span></span>
 <span><span class="co">##  ENSG00000171603 0.43102027  0.298698  18.12310  -123.212     0.019   2.07433</span></span>
 <span><span class="co">##  ENSG00000162545 0.15373440  0.547736   2.38046  -119.576     0.014   2.63576</span></span>
 <span><span class="co">##                        var     spcov   prop_sv loglik_lm   LR_stat      rank</span></span>
@@ -548,12 +548,12 @@ <h1 class="title"><span id="sec-feature-selection" class="quarto-section-identif
 <span><span class="co">##  ENSG00000160307 ENSG00000160307       S100B Gene Expression        FALSE</span></span>
 <span><span class="co">##                   sigma.sq    tau.sq       phi    loglik   runtime      mean</span></span>
 <span><span class="co">##                  &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt;</span></span>
-<span><span class="co">##  ENSG00000197971   3.92430  0.175336   0.93014  -118.372     0.020   3.78073</span></span>
-<span><span class="co">##  ENSG00000123560   3.23544  0.461590   1.03983  -140.269     0.016   2.86143</span></span>
-<span><span class="co">##  ENSG00000109846   1.89968  0.281795   1.88555  -126.692     0.021   1.86058</span></span>
+<span><span class="co">##  ENSG00000197971   3.92430  0.175336   0.93014  -118.372     0.019   3.78073</span></span>
+<span><span class="co">##  ENSG00000123560   3.23544  0.461590   1.03983  -140.269     0.017   2.86143</span></span>
+<span><span class="co">##  ENSG00000109846   1.89968  0.281795   1.88555  -126.692     0.015   1.86058</span></span>
 <span><span class="co">##  ENSG00000173786   2.28793  0.402524   1.02675  -129.206     0.015   1.79558</span></span>
-<span><span class="co">##  ENSG00000131095   2.23709  0.461297   2.49083  -149.004     0.017   1.94543</span></span>
-<span><span class="co">##  ENSG00000160307   1.24179  0.155737   5.76279  -129.722     0.013   1.82695</span></span>
+<span><span class="co">##  ENSG00000131095   2.23709  0.461297   2.49083  -149.004     0.023   1.94543</span></span>
+<span><span class="co">##  ENSG00000160307   1.24179  0.155737   5.76279  -129.722     0.014   1.82695</span></span>
 <span><span class="co">##                        var     spcov   prop_sv loglik_lm   LR_stat      rank</span></span>
 <span><span class="co">##                  &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt;</span></span>
 <span><span class="co">##  ENSG00000197971   2.76535  0.523969  0.957231  -192.250  147.7556         1</span></span>

docs/devel/pages/human-dlpfc-workflow.html

@@ -701,12 +701,12 @@ <h1 class="title"><span id="sec-human-dlpfc-workflow" class="quarto-section-iden
 <span><span class="co">##  ENSG00000160307 ENSG00000160307       S100B Gene Expression        FALSE</span></span>
 <span><span class="co">##                   sigma.sq    tau.sq       phi    loglik   runtime      mean</span></span>
 <span><span class="co">##                  &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt;</span></span>
-<span><span class="co">##  ENSG00000197971   3.92430  0.175336   0.93014  -118.372     0.019   3.78073</span></span>
+<span><span class="co">##  ENSG00000197971   3.92430  0.175336   0.93014  -118.372     0.020   3.78073</span></span>
 <span><span class="co">##  ENSG00000123560   3.23544  0.461590   1.03983  -140.269     0.016   2.86143</span></span>
 <span><span class="co">##  ENSG00000109846   1.89968  0.281795   1.88555  -126.692     0.015   1.86058</span></span>
 <span><span class="co">##  ENSG00000173786   2.28793  0.402524   1.02675  -129.206     0.015   1.79558</span></span>
-<span><span class="co">##  ENSG00000131095   2.23709  0.461297   2.49083  -149.004     0.016   1.94543</span></span>
-<span><span class="co">##  ENSG00000160307   1.24179  0.155737   5.76279  -129.722     0.014   1.82695</span></span>
+<span><span class="co">##  ENSG00000131095   2.23709  0.461297   2.49083  -149.004     0.017   1.94543</span></span>
+<span><span class="co">##  ENSG00000160307   1.24179  0.155737   5.76279  -129.722     0.013   1.82695</span></span>
 <span><span class="co">##                        var     spcov   prop_sv loglik_lm   LR_stat      rank</span></span>
 <span><span class="co">##                  &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt;</span></span>
 <span><span class="co">##  ENSG00000197971   2.76535  0.523969  0.957231  -192.250  147.7556         1</span></span>

docs/devel/pages/mouse-coronal-workflow.html

@@ -686,9 +686,9 @@ <h1 class="title"><span id="sec-mouse-coronal-workflow" class="quarto-section-id
 <span><span class="co">##  ENSMUSG00000046330        FALSE 0.0549986 0.1133114   6.47579  -48.2811</span></span>
 <span><span class="co">##                       runtime      mean       var     spcov   prop_sv</span></span>
 <span><span class="co">##                     &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt;</span></span>
-<span><span class="co">##  ENSMUSG00000061518     0.026   4.98425  0.142977 0.0291204  0.149022</span></span>
+<span><span class="co">##  ENSMUSG00000061518     0.021   4.98425  0.142977 0.0291204  0.149022</span></span>
 <span><span class="co">##  ENSMUSG00000073702     0.012   4.83432  0.143616 0.0542917  0.444515</span></span>
-<span><span class="co">##  ENSMUSG00000046330     0.014   5.35620  0.166734 0.0437844  0.326770</span></span>
+<span><span class="co">##  ENSMUSG00000046330     0.015   5.35620  0.166734 0.0437844  0.326770</span></span>
 <span><span class="co">##                     loglik_lm   LR_stat      rank      pval      padj</span></span>
 <span><span class="co">##                     &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt;</span></span>
 <span><span class="co">##  ENSMUSG00000061518  -44.1377  0.981135       184 0.6122789 0.6588653</span></span>
@@ -723,9 +723,9 @@ <h1 class="title"><span id="sec-mouse-coronal-workflow" class="quarto-section-id
 <span><span class="co">##                       runtime      mean       var     spcov   prop_sv</span></span>
 <span><span class="co">##                     &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt; &lt;numeric&gt;</span></span>
 <span><span class="co">##  ENSMUSG00000046447     0.018   5.35338   1.50820  0.256357  0.967714</span></span>
-<span><span class="co">##  ENSMUSG00000053310     0.020   4.85871   3.71912  0.366737  0.927612</span></span>
-<span><span class="co">##  ENSMUSG00000018593     0.020   3.61331   1.87664  0.395442  0.963966</span></span>
-<span><span class="co">##  ENSMUSG00000032532     0.017   4.19282   2.72400  0.411820  1.000000</span></span>
+<span><span class="co">##  ENSMUSG00000053310     0.019   4.85871   3.71912  0.366737  0.927612</span></span>
+<span><span class="co">##  ENSMUSG00000018593     0.019   3.61331   1.87664  0.395442  0.963966</span></span>
+<span><span class="co">##  ENSMUSG00000032532     0.016   4.19282   2.72400  0.411820  1.000000</span></span>
 <span><span class="co">##  ENSMUSG00000070570     0.015   3.62933   3.00604  0.447757  0.891889</span></span>
 <span><span class="co">##  ENSMUSG00000024617     0.022   4.11652   1.17870  0.288711  0.935123</span></span>
 <span><span class="co">##                     loglik_lm   LR_stat      rank        pval        padj</span></span>

docs/devel/pages/preamble.html

@@ -737,7 +737,7 @@ <h1 class="title">Preamble</h1>
 <span><span class="co">##   zip                    2.3.1     2024-01-27 [2] RSPM (R 4.4.0)</span></span>
 <span><span class="co">##   zlibbioc               1.51.1    2024-06-05 [2] Bioconductor 3.20 (R 4.4.0)</span></span>
 <span><span class="co">##  </span></span>
-<span><span class="co">##   [1] /tmp/RtmpVgWQ4p/Rinst8c21afd630</span></span>
+<span><span class="co">##   [1] /tmp/RtmpbBbNyF/Rinst8cfaa71a6</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>

docs/devel/pages/spatialibd-workflow.html

@@ -631,7 +631,7 @@ <h1 class="title"><span id="sec-spatiallibd-workflow" class="quarto-section-iden
 <span><span class="co">## How long this code took to run</span></span>
 <span><span class="va">time_prereqs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">time_prereqs</span> <span class="op">-</span> <span class="va">time_start</span></span>
-<span><span class="co">##  Time difference of 1.439684 mins</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span><span class="co">##  Time difference of 1.457038 mins</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 </section><section id="prepare-for-spatiallibd" class="level2" data-number="17.4"><h2 data-number="17.4" class="anchored" data-anchor-id="prepare-for-spatiallibd">
 <span class="header-section-number">17.4</span> Prepare for spatialLIBD</h2>
@@ -662,7 +662,7 @@ <h1 class="title"><span id="sec-spatiallibd-workflow" class="quarto-section-iden
 <span><span class="co">## Show the GTF cache location</span></span>
 <span><span class="va">gtf_cache</span></span>
 <span><span class="co">##                                                                      BFC1 </span></span>
-<span><span class="co">##  "/root/.cache/R/BiocFileCache/6bc2eadca4c_gencode.v32.annotation.gtf.gz"</span></span>
+<span><span class="co">##  "/root/.cache/R/BiocFileCache/6bc2afffb37_gencode.v32.annotation.gtf.gz"</span></span>
 <span></span>
 <span><span class="co">## Import into R (takes ~1 min)</span></span>
 <span><span class="va">gtf</span> <span class="op">&lt;-</span> <span class="fu">rtracklayer</span><span class="fu">::</span><span class="fu">import</span><span class="op">(</span><span class="va">gtf_cache</span><span class="op">)</span></span>
@@ -829,9 +829,9 @@ <h1 class="title"><span id="sec-spatiallibd-workflow" class="quarto-section-iden
 <span></span>
 <span><span class="co">## How long this code took to run</span></span>
 <span><span class="va">time_end</span> <span class="op">-</span> <span class="va">time_prereqs</span></span>
-<span><span class="co">##  Time difference of 1.143132 mins</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span><span class="co">##  Time difference of 34.90911 secs</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
-<p>Creating our final <code>spe</code> object took 2.58281671603521 to run. So you might want to save this object for later use.</p>
+<p>Creating our final <code>spe</code> object took 2.03885692358017 to run. So you might want to save this object for later use.</p>
 <div class="cell" data-layout-align="center">
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html">saveRDS</a></span><span class="op">(</span><span class="va">spe</span>, file <span class="op">=</span> <span class="st">"spe_workflow_Visium_spatialLIBD.rds"</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
@@ -1269,7 +1269,7 @@ <h1 class="title"><span id="sec-spatiallibd-workflow" class="quarto-section-iden
 <span><span class="co">##   yaml                   2.3.10    2024-07-26 [2] RSPM (R 4.4.0)</span></span>
 <span><span class="co">##   zlibbioc               1.51.1    2024-06-05 [2] Bioconductor 3.20 (R 4.4.0)</span></span>
 <span><span class="co">##  </span></span>
-<span><span class="co">##   [1] /tmp/RtmpVgWQ4p/Rinst8c21afd630</span></span>
+<span><span class="co">##   [1] /tmp/RtmpbBbNyF/Rinst8cfaa71a6</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>