remove R script ngsupload

cox-labs · Nov 28, 2024 · 8e9bc21 · 8e9bc21
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diff --git a/docs/htseqvsperseus.table.rar b/docs/htseqvsperseus.table.rar
diff --git a/docs/ngsupload.html b/docs/ngsupload.html
@@ -22,40 +22,6 @@
   margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
   vertical-align: middle;
 }
-/* CSS for syntax highlighting */
-pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { line-height: 1.25; }
-pre > code.sourceCode > span:empty { height: 1.2em; }
-.sourceCode { overflow: visible; }
-code.sourceCode > span { color: inherit; text-decoration: inherit; }
-div.sourceCode { margin: 1em 0; }
-pre.sourceCode { margin: 0; }
-@media screen {
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-}
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-    -khtml-user-select: none; -moz-user-select: none;
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 /* CSS for citations */
 div.csl-bib-body { }
 div.csl-entry {
@@ -476,20 +442,19 @@ <h1 data-number="7"><span class="header-section-number">7</span> Comparison with
 </figcaption>
 </figure>
 </div>
-<p><code>HTSeq-count</code> <span class="citation" data-cites="anders2014">(<a href="#ref-anders2014" role="doc-biblioref">Anders, Pyl, and Huber 2014</a>)</span> is part of the HTSeq suite, a python library to facilitate and represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls. <code>htseq-count</code> can be used to pre-processes RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. To recreate the plot, one can download the data table below <span class="citation" data-cites="downloadthis">(<a href="#ref-downloadthis" role="doc-biblioref">Mattioni Maturana 2022</a>)</span></p>
-<div class="cell">
-<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># remotes::install_github("fmmattioni/downloadthis")</span></span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(downloadthis)</span>
-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">download_file</span>(</span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">path =</span> <span class="st">"htseqvsperseus.table.rar"</span>,</span>
-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">output_name =</span> <span class="st">"HTSeq vs. Persues Table"</span>,</span>
-<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">button_label =</span> <span class="st">"Download data table"</span>,</span>
-<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">button_type =</span> <span class="st">"info"</span>,</span>
-<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a>  <span class="at">has_icon =</span> <span class="cn">TRUE</span>,</span>
-<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>  <span class="at">icon =</span> <span class="st">"fa fa-save"</span>,</span>
-<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a>  <span class="at">self_contained =</span> <span class="cn">FALSE</span></span>
-<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-</div>
+<p><code>HTSeq-count</code> <span class="citation" data-cites="anders2014">(<a href="#ref-anders2014" role="doc-biblioref">Anders, Pyl, and Huber 2014</a>)</span> is part of the HTSeq suite, a python library to facilitate and represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls. <code>htseq-count</code> can be used to pre-processes RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. To recreate the plot, one can download the <a href="htseqvsperseus.table.rar">data table</a> below <span class="citation" data-cites="downloadthis">(<a href="#ref-downloadthis" role="doc-biblioref">Mattioni Maturana 2022</a>)</span></p>
+<pre><code>
+# remotes::install_github("fmmattioni/downloadthis")
+library(downloadthis)
+download_file(
+  path = "htseqvsperseus.table.rar",
+  output_name = "HTSeq vs. Persues Table",
+  button_label = "Download data table",
+  button_type = "info",
+  has_icon = TRUE,
+  icon = "fa fa-save",
+  self_contained = FALSE
+)</code></pre>
 <!-- ==== Parameters specific for "Chromatin IP" experiment ====
 The most popular way to deal with Chromatin IP experiment is sequence relatively small part of a read - enough for unique alignment - and already in silico extend such read until expected length.
 {{ :user:activities:matrixupload:chipseqextend.png?500 |}}

diff --git a/ngsupload.qmd b/ngsupload.qmd
@@ -134,11 +134,9 @@ Specifies the number of used threads for uploading NGS data.
 
 ![Comparing HTSeq-counts against Perseus](images/htseqvsperseus.multiscatter.png){#fig-htseqvsperseus}
 
-`HTSeq-count` [@anders2014] is part of the HTSeq suite, a python library to facilitate and represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls. `htseq-count` can be used to pre-processes RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. To recreate the plot, one can download the data table below [@downloadthis]
+`HTSeq-count` [@anders2014] is part of the HTSeq suite, a python library to facilitate and represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls. `htseq-count` can be used to pre-processes RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. To recreate the plot, one can download the [data table](htseqvsperseus.table.rar) below [@downloadthis] 
 
-```{r}
-#| echo: true
-#| eval: false
+```
 
 # remotes::install_github("fmmattioni/downloadthis")
 library(downloadthis)